- galaxy-user - lists.galaxyproject.org

where are my deleted datasets?
by Erick Antezana 12 Apr '10

12 Apr '10

Hi, I managed to enable the possibility to 'Add datasets' via the 'Upload directory of files' option for non-admin users. It works fine: I can import (as admin and non-admin user) specific datasets into my history (copy and/or no-copy) so that I could launch some tools over them, etc. However, if I delete a specific dataset (as admin) that was imported as non-admin and then login again as non-admin, I can still see the imported datasets in my history pane. Where is actually located the reference to the (deleted) dataset? I was able to find the copied files at .../database/files/000/* , these will be cleaned out (if deleted) by the purge scripts eventually... I am using SQLAlchemy with mysql for the DB connection. cheers, Erick

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Setting default access permission for datasets and histories
by H. Mei 12 Apr '10

12 Apr '10

Dear galaxy team, The possibility of setting default dataset/history permission (e.g. "Change default permissions for the current history") is mentioned in the page of http://bitbucket.org/galaxy/galaxy-central/wiki/SecurityFeatures. However I can't find it in the "Options" dropdown on Galaxy UI. Am I looking at a wrong place? The link http://www.bx.psu.edu/trac/local/manage_history_defaults.png is also broken. Best, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center (http://www.nbic.nl/) Skype: leon_mei Mobile: +31 6 41709231

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Sequence logo
by Erick Antezana 12 Apr '10

12 Apr '10

Hi, is there any Galaxy tool supporting the display of "sequence logos" (http://en.wikipedia.org/wiki/Sequence_logo) ? thanks, Erick

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Including mothur?
by Rohan Sachdeva 10 Apr '10

10 Apr '10

Hi All, I'm a microbial ecologist and use mothur a ton. It's a C++ commandline program that does lots of things that I think would work great in galaxy. Like trimming, barcode sorting, aligning, OTU calling, ecology stats, heatmap/diagram creation. Here's a link http://www.mothur.org/ Rohan

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how to turn on debug?
by Peter Andrews 09 Apr '10

09 Apr '10

I received a server error and would like to more detailed information Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) How do I 'turn debug on'?. I am using the public galaxy instance http://main.g2.bx.psu.edu/ Thanks, Peter Andrews -- -------------- Peter Andrews Programmer Computational Genetics Lab Dartmouth Hitchcock Medical Center (603) 653-9963

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Galaxy Instance
by Sonali Thakur 09 Apr '10

09 Apr '10

Could you please let me from where I can clone the latest galaxy? I tried cloning from below two and get the same revision. hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist hg clone https://bitbucket.org/galaxy/galaxy-dist/ I am not getting the one which we can see at http://main.g2.bx.psu.edu/root Please suggest. Regards -Sonali

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New select random lines tool available on test
by Kanwei Li 09 Apr '10

09 Apr '10

Dear users, I have created a new tool to randomly extract random lines from a dataset as some of you have requested it. It is now available in the repository and on our public test instance under "Text Manipulation". Any feedback is appreciated. Thanks, Kanwei

2 1

Internal Server Error
by Rathi Thiagarajan 09 Apr '10

09 Apr '10

Hi there, Just letting you know that there appears to be an internal server error. Time: 7:30pm EDT Thursday 8th of April Cheers Rathi

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Re: [galaxy-user] galaxy-user Digest, Vol 46, Issue 5
by Peter Andrews 08 Apr '10

08 Apr '10

I also find that uploading a file rarely works -- it just displays the loading up blue arrow forever. On 4/7/2010 9:23 PM, galaxy-user-request(a)lists.bx.psu.edu wrote: > Send galaxy-user mailing list submissions to > galaxy-user(a)lists.bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-user > or, via email, send a message with subject or body 'help' to > galaxy-user-request(a)lists.bx.psu.edu > > You can reach the person managing the list at > galaxy-user-owner(a)lists.bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-user digest..." > > > Today's Topics: > > 1. Re: Upload file (Daniel Blankenberg) > 2. Re: Upload file (Yanwei Tan) > 3. Re: Upload file (Daniel Blankenberg) > 4. Problem w/Cheetah, repeating dataset input (Jesse Erdmann) > 5. Re: Quality based trimming (Florent Angly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 7 Apr 2010 09:53:19 -0400 > From: Daniel Blankenberg<dan(a)bx.psu.edu> > To: Yanwei Tan<Tan(a)nbio.uni-heidelberg.de> > Cc:galaxy-user@lists.bx.psu.edu > Subject: Re: [galaxy-user] Upload file > Message-ID:<37031484-8E2E-4A9C-A027-D0D75F8D0799(a)bx.psu.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Wei, > > 3Gb is not that large of a file and should upload without issue. How are you uploading the file? - May I suggest that you try placing the file in a web-accessable location and provide the url to the upload tool in the paste box. > > Galaxy does accept the upload of individual gzipped files which can greatly reduce the time required for the transfer. > > Thanks, > > Dan > > > On Apr 6, 2010, at 6:04 PM, Yanwei Tan wrote: > > >> Hi Dan, >> >> Here I met a problem regarding the speed of upload file into Galaxy. Since my data is around 3G fastq file, I uploaded two days ago, the uploading still did not finish yet. I was wondering if I should try the zip compressed file. >> >> Many thanks! >> Wei >> >> On 4/6/10 5:00 PM, Daniel Blankenberg wrote: >> >>> Hi Florent, >>> >>> Thanks very much for the comments. A sliding window sounds like an excellent approach: allow users to specify the window size, step size, an aggregation action to perform on the window (min, max, sum, mean, etc ), a comparison method (<,<=, ==, etc) and a threshold quality value; allowing users to specify the ends (both or only one or the other) to trim would also likely be useful. Would it also be desirable to allow specifying a number of quality scores that can be excluded from the aggregation action (the zero low quality base pairs in your example)? A window size of 1 would handle the simple case of only trimming the very ends while allowing the user to configure more complex windowing schemes. Thoughts? >>> >>> Thanks, >>> >>> Dan >>> >>> On Apr 6, 2010, at 4:00 AM, Florent Angly wrote: >>> >>> >>> >>>> Thanks for your reply Daniel. >>>> >>>> >>>>> You are correct that there is not currently a tool to trim directly by quality in Galaxy; currently the the Summary statistics and boxplot tools are used to determine good cut off for use in the trim by column tool; percentage of read length can be more useful on variable length reads. However, adding a tool that can directly trim reads based upon a threshold quality score seems like a natural fit for Galaxy, when uniform read length is not present at the start and/or not a requirement at the end and the percentage-of-read-length method is not sufficient >>>>> >>>>> >>>>> >>>> That's right... I did not even think about using the boxplot tool to find how much to trim the ends. My reads all have the same length, but still, is seems more natural to only trim as much as needed and no more. For example, I have some reads that are completely low quality and should entirely trimmed/removed, whereas some might of good quality over almost all their length. >>>> >>>> >>>> >>>>> Lets verify that you are looking for something like this, where 'x' is a low quality base and 'o' is a high quality base: >>>>> Start with: >>>>> xxxooooxxooooxxx >>>>> after trimming ends for 'x': >>>>> ooooxxoooo >>>>> So that trimming happens only from the ends and stops as soon as a base above the threshold is found and internal low quality bases are not considered. >>>>> >>>>> >>>>> >>>> It's probaby better to use a short sliding window (of, say, 5 bp) and trim the ends until the window has no more than, say zero low quality base pairs. So, the following sequence would be converted from: >>>> xxxoxooooooxxooooooxoxxx >>>> to: >>>> ooooooxxoooooo >>>> >>>> Florent >>>> >>>> _______________________________________________ >>>> galaxy-user mailing list >>>> galaxy-user(a)lists.bx.psu.edu >>>> http://lists.bx.psu.edu/listinfo/galaxy-user >>>> >>>> >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >>> >>> >> -- >> Yanwei Tan >> Institute of Neurobiology >> 1.OG, AG Bading >> Im Neuenheimer Feld 364 >> University of Heidelberg >> 69120 Heidelberg >> Germany >> >> Tel:+49-6221-548319 >> Fax:+49-6221-546700 >> >> > > > ------------------------------ > > Message: 2 > Date: Wed, 07 Apr 2010 17:21:37 +0200 > From: Yanwei Tan<Tan(a)nbio.uni-heidelberg.de> > To: Daniel Blankenberg<dan(a)bx.psu.edu> > Cc:galaxy-user@lists.bx.psu.edu > Subject: Re: [galaxy-user] Upload file > Message-ID:<4BBCA301.80907(a)nbio.uni-heidelberg.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Dan, > > Many thanks for your reply. I just upload the file from my computer and > browse the location. If I upload the zip compressed file, should I > choose txtseq.zip format? My data is fastq file in txt file. And how > could I put the file in a web-accessible location? You mean the FTP server? > > Thanks for your help! > Wei > > > On 4/7/10 3:53 PM, Daniel Blankenberg wrote: > >> Hi Wei, >> >> 3Gb is not that large of a file and should upload without issue. How are you uploading the file? - May I suggest that you try placing the file in a web-accessable location and provide the url to the upload tool in the paste box. >> >> Galaxy does accept the upload of individual gzipped files which can greatly reduce the time required for the transfer. >> >> Thanks, >> >> Dan >> >> >> On Apr 6, 2010, at 6:04 PM, Yanwei Tan wrote: >> >> >> >>> Hi Dan, >>> >>> Here I met a problem regarding the speed of upload file into Galaxy. Since my data is around 3G fastq file, I uploaded two days ago, the uploading still did not finish yet. I was wondering if I should try the zip compressed file. >>> >>> Many thanks! >>> Wei >>> >>> On 4/6/10 5:00 PM, Daniel Blankenberg wrote: >>> >>> >>>> Hi Florent, >>>> >>>> Thanks very much for the comments. A sliding window sounds like an excellent approach: allow users to specify the window size, step size, an aggregation action to perform on the window (min, max, sum, mean, etc ), a comparison method (<,<=, ==, etc) and a threshold quality value; allowing users to specify the ends (both or only one or the other) to trim would also likely be useful. Would it also be desirable to allow specifying a number of quality scores that can be excluded from the aggregation action (the zero low quality base pairs in your example)? A window size of 1 would handle the simple case of only trimming the very ends while allowing the user to configure more complex windowing schemes. Thoughts? >>>> >>>> Thanks, >>>> >>>> Dan >>>> >>>> On Apr 6, 2010, at 4:00 AM, Florent Angly wrote: >>>> >>>> >>>> >>>> >>>>> Thanks for your reply Daniel. >>>>> >>>>> >>>>> >>>>>> You are correct that there is not currently a tool to trim directly by quality in Galaxy; currently the the Summary statistics and boxplot tools are used to determine good cut off for use in the trim by column tool; percentage of read length can be more useful on variable length reads. However, adding a tool that can directly trim reads based upon a threshold quality score seems like a natural fit for Galaxy, when uniform read length is not present at the start and/or not a requirement at the end and the percentage-of-read-length method is not sufficient >>>>>> >>>>>> >>>>>> >>>>>> >>>>> That's right... I did not even think about using the boxplot tool to find how much to trim the ends. My reads all have the same length, but still, is seems more natural to only trim as much as needed and no more. For example, I have some reads that are completely low quality and should entirely trimmed/removed, whereas some might of good quality over almost all their length. >>>>> >>>>> >>>>> >>>>> >>>>>> Lets verify that you are looking for something like this, where 'x' is a low quality base and 'o' is a high quality base: >>>>>> Start with: >>>>>> xxxooooxxooooxxx >>>>>> after trimming ends for 'x': >>>>>> ooooxxoooo >>>>>> So that trimming happens only from the ends and stops as soon as a base above the threshold is found and internal low quality bases are not considered. >>>>>> >>>>>> >>>>>> >>>>>> >>>>> It's probaby better to use a short sliding window (of, say, 5 bp) and trim the ends until the window has no more than, say zero low quality base pairs. So, the following sequence would be converted from: >>>>> xxxoxooooooxxooooooxoxxx >>>>> to: >>>>> ooooooxxoooooo >>>>> >>>>> Florent >>>>> >>>>> _______________________________________________ >>>>> galaxy-user mailing list >>>>> galaxy-user(a)lists.bx.psu.edu >>>>> http://lists.bx.psu.edu/listinfo/galaxy-user >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> galaxy-user mailing list >>>> galaxy-user(a)lists.bx.psu.edu >>>> http://lists.bx.psu.edu/listinfo/galaxy-user >>>> >>>> >>>> >>> >>> >> >> > > > ------------------------------ > > Message: 3 > Date: Wed, 7 Apr 2010 11:32:05 -0400 > From: Daniel Blankenberg<dan(a)bx.psu.edu> > To: Yanwei Tan<Tan(a)nbio.uni-heidelberg.de> > Cc:galaxy-user@lists.bx.psu.edu > Subject: Re: [galaxy-user] Upload file > Message-ID:<54E8CB9D-5C36-4A20-8C8A-188B3F908012(a)bx.psu.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Wei, > > To upload a gzipped file (e.g. somefile.fastq.gz), just upload as you normally would (don't set to txtseq.zip - this is a special format), the file will be ungzipped automatically; zip files are not yet supported. > > As far as a web-accessible location, you can specify http(s) and ftp locations by entering e.g.http://someserver.org/somefile.fastq orftp://someserver.org/somefile.fastq into the 'paste' box in the upload tool, if you have access this type of resource. > > Thanks, > > Dan > > > On Apr 7, 2010, at 11:21 AM, Yanwei Tan wrote: > > >> Hi Dan, >> >> Many thanks for your reply. I just upload the file from my computer and browse the location. If I upload the zip compressed file, should I choose txtseq.zip format? My data is fastq file in txt file. And how could I put the file in a web-accessible location? You mean the FTP server? >> >> Thanks for your help! >> Wei >> >> >> On 4/7/10 3:53 PM, Daniel Blankenberg wrote: >> >>> Hi Wei, >>> >>> 3Gb is not that large of a file and should upload without issue. How are you uploading the file? - May I suggest that you try placing the file in a web-accessable location and provide the url to the upload tool in the paste box. >>> >>> Galaxy does accept the upload of individual gzipped files which can greatly reduce the time required for the transfer. >>> >>> Thanks, >>> >>> Dan >>> >>> >>> On Apr 6, 2010, at 6:04 PM, Yanwei Tan wrote: >>> >>> >>> >>>> Hi Dan, >>>> >>>> Here I met a problem regarding the speed of upload file into Galaxy. Since my data is around 3G fastq file, I uploaded two days ago, the uploading still did not finish yet. I was wondering if I should try the zip compressed file. >>>> >>>> Many thanks! >>>> Wei >>>> >>>> On 4/6/10 5:00 PM, Daniel Blankenberg wrote: >>>> >>>> >>>>> Hi Florent, >>>>> >>>>> Thanks very much for the comments. A sliding window sounds like an excellent approach: allow users to specify the window size, step size, an aggregation action to perform on the window (min, max, sum, mean, etc ), a comparison method (<,<=, ==, etc) and a threshold quality value; allowing users to specify the ends (both or only one or the other) to trim would also likely be useful. Would it also be desirable to allow specifying a number of quality scores that can be excluded from the aggregation action (the zero low quality base pairs in your example)? A window size of 1 would handle the simple case of only trimming the very ends while allowing the user to configure more complex windowing schemes. Thoughts? >>>>> >>>>> Thanks, >>>>> >>>>> Dan >>>>> >>>>> On Apr 6, 2010, at 4:00 AM, Florent Angly wrote: >>>>> >>>>> >>>>> >>>>> >>>>>> Thanks for your reply Daniel. >>>>>> >>>>>> >>>>>> >>>>>>> You are correct that there is not currently a tool to trim directly by quality in Galaxy; currently the the Summary statistics and boxplot tools are used to determine good cut off for use in the trim by column tool; percentage of read length can be more useful on variable length reads. However, adding a tool that can directly trim reads based upon a threshold quality score seems like a natural fit for Galaxy, when uniform read length is not present at the start and/or not a requirement at the end and the percentage-of-read-length method is not sufficient >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> That's right... I did not even think about using the boxplot tool to find how much to trim the ends. My reads all have the same length, but still, is seems more natural to only trim as much as needed and no more. For example, I have some reads that are completely low quality and should entirely trimmed/removed, whereas some might of good quality over almost all their length. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Lets verify that you are looking for something like this, where 'x' is a low quality base and 'o' is a high quality base: >>>>>>> Start with: >>>>>>> xxxooooxxooooxxx >>>>>>> after trimming ends for 'x': >>>>>>> ooooxxoooo >>>>>>> So that trimming happens only from the ends and stops as soon as a base above the threshold is found and internal low quality bases are not considered. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> It's probaby better to use a short sliding window (of, say, 5 bp) and trim the ends until the window has no more than, say zero low quality base pairs. So, the following sequence would be converted from: >>>>>> xxxoxooooooxxooooooxoxxx >>>>>> to: >>>>>> ooooooxxoooooo >>>>>> >>>>>> Florent >>>>>> >>>>>> _______________________________________________ >>>>>> galaxy-user mailing list >>>>>> galaxy-user(a)lists.bx.psu.edu >>>>>> http://lists.bx.psu.edu/listinfo/galaxy-user >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> galaxy-user mailing list >>>>> galaxy-user(a)lists.bx.psu.edu >>>>> http://lists.bx.psu.edu/listinfo/galaxy-user >>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> > > > ------------------------------ > > Message: 4 > Date: Wed, 7 Apr 2010 16:25:37 -0500 > From: Jesse Erdmann<jerdmann(a)umn.edu> > To:galaxy-user@bx.psu.edu > Subject: [galaxy-user] Problem w/Cheetah, repeating dataset input > Message-ID: > <m2h97174eb21004071425o9cba9384i648744371304d210(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > I'm using the following XML: > > ... > <inputs> > <param type="data" format="txt" name="seqmeta" label="PAPS.seqmeta"/> > <param type="data" format="txt" name="lib_info" label="Label Info"/> > <repeat name="to_merge" title="Evaluation Inputs and Results"> > <param type="select" name="pmm" label="Mismatch %" help="Maximum > % of mismatch between the construct sequence and the comparison > sequence."> > <option value="10">10%</option> > <option value="15">15%</option> > <option value="20">20%</option> > </param> > <param type="text" name="max_length" label="Max Construct Length" > value="25" /> > <param format="fasta" name="fasta_in" type="data" label="FastA Output"/> > <param format="txt" name="seq_stats" type="data" label="Sequence Stats"/> > </repeat> > </inputs> > ... > <configfiles> > <configfile name="file_info"> > #for $merge_set in enumerate( $to_merge ) > #silent sys.stderr.write($merge_set.__str__() + "\n") > #silent sys.stderr.write($merge_set.fasta_in.__str__()) > #end for > </configfile> > </configfiles> > ... > > And getting the resulting output: > > 127.0.0.1 - - [07/Apr/2010:15:31:50 -0500] "POST /admin/tool_reload > HTTP/1.1" 200 -"http://localhost:8080/admin/reload_tool" "Mozilla/5.0 > (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 > Firefox/3.6.2" > 127.0.0.1 - - [07/Apr/2010:15:31:59 -0500] "POST /tool_runner/index > HTTP/1.1" 200 -"http://localhost:8080/tool_runner/index" "Mozilla/5.0 > (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 > Firefox/3.6.2" > galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-04-07 15:32:03,765 > RoundRobin queue: user/session did not exist, created new jobqueue for > session = 6 > galaxy.jobs DEBUG 2010-04-07 15:32:03,766 job 234 put in policy queue > galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-04-07 15:32:03,766 > RoundRobin queue: retrieving job from job queue for session = 6 > galaxy.jobs DEBUG 2010-04-07 15:32:03,766 dispatching job 234 to local runner > galaxy.jobs DEBUG 2010-04-07 15:32:05,423 job 234 dispatched > (0, {'seq_stats':<galaxy.tools.DatasetFilenameWrapper object at > 0x572b390>, '__index__': 0, 'max_length': > <galaxy.tools.InputValueWrapper object at 0x572b8d0>, 'fasta_in': > <galaxy.tools.DatasetFilenameWrapper object at 0x572b810>, 'pmm': > <galaxy.tools.SelectToolParameterWrapper object at 0x572b290>}) > 127.0.0.1 - - [07/Apr/2010:15:32:03 -0500] "GET /history HTTP/1.1" 200 > -"http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; > U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 > Firefox/3.6.2" > galaxy.jobs.runners.local ERROR 2010-04-07 15:32:07,356 failure running job 234 > Traceback (most recent call last): > File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/jobs/runners/local.py", > line 55, in run_job > job_wrapper.prepare() > File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/jobs/__init__.py", > line 386, in prepare > config_filenames = self.tool.build_config_files( param_dict, > self.working_directory ) > File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/tools/__init__.py", > line 1364, in build_config_files > f.write( fill_template( template_text, context=param_dict ) ) > File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/util/template.py", > line 9, in fill_template > return str( Template( source=template_text, searchList=[context] ) ) > File "/Users/jerdmann/Python/galaxy-central/eggs/Cheetah-2.2.2-py2.5-macosx-10.3-fat-ucs2.egg/Cheetah/Template.py", > line 1004, in __str__ > return getattr(self, mainMethName)() > File "cheetah_DynamicallyCompiledCheetahTemplate_1270672326_31_15888.py", > line 86, in respond > NotFound: cannot find 'fasta_in' while searching for 'merge_set.fasta_in' > > So, I'm printing the merge_set dictionary and seeing a fasta_in key, > but when I try to use fasta_in it can not be found. I'm assuming this > is probably a syntax oversight on my part, but I'm not seeing it. > > -- -------------- Peter Andrews Programmer Computational Genetics Lab Dartmouth Hitchcock Medical Center (603) 653-9963

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Re: [galaxy-user] Upload file
by Daniel Blankenberg 07 Apr '10

07 Apr '10

Hi Wei, 3Gb is not that large of a file and should upload without issue. How are you uploading the file? - May I suggest that you try placing the file in a web-accessable location and provide the url to the upload tool in the paste box. Galaxy does accept the upload of individual gzipped files which can greatly reduce the time required for the transfer. Thanks, Dan On Apr 6, 2010, at 6:04 PM, Yanwei Tan wrote: > Hi Dan, > > Here I met a problem regarding the speed of upload file into Galaxy. Since my data is around 3G fastq file, I uploaded two days ago, the uploading still did not finish yet. I was wondering if I should try the zip compressed file. > > Many thanks! > Wei > > On 4/6/10 5:00 PM, Daniel Blankenberg wrote: >> Hi Florent, >> >> Thanks very much for the comments. A sliding window sounds like an excellent approach: allow users to specify the window size, step size, an aggregation action to perform on the window (min, max, sum, mean, etc ), a comparison method (<,<=, ==, etc) and a threshold quality value; allowing users to specify the ends (both or only one or the other) to trim would also likely be useful. Would it also be desirable to allow specifying a number of quality scores that can be excluded from the aggregation action (the zero low quality base pairs in your example)? A window size of 1 would handle the simple case of only trimming the very ends while allowing the user to configure more complex windowing schemes. Thoughts? >> >> Thanks, >> >> Dan >> >> On Apr 6, 2010, at 4:00 AM, Florent Angly wrote: >> >> >>> Thanks for your reply Daniel. >>> >>>> You are correct that there is not currently a tool to trim directly by quality in Galaxy; currently the the Summary statistics and boxplot tools are used to determine good cut off for use in the trim by column tool; percentage of read length can be more useful on variable length reads. However, adding a tool that can directly trim reads based upon a threshold quality score seems like a natural fit for Galaxy, when uniform read length is not present at the start and/or not a requirement at the end and the percentage-of-read-length method is not sufficient >>>> >>>> >>> That's right... I did not even think about using the boxplot tool to find how much to trim the ends. My reads all have the same length, but still, is seems more natural to only trim as much as needed and no more. For example, I have some reads that are completely low quality and should entirely trimmed/removed, whereas some might of good quality over almost all their length. >>> >>> >>>> Lets verify that you are looking for something like this, where 'x' is a low quality base and 'o' is a high quality base: >>>> Start with: >>>> xxxooooxxooooxxx >>>> after trimming ends for 'x': >>>> ooooxxoooo >>>> So that trimming happens only from the ends and stops as soon as a base above the threshold is found and internal low quality bases are not considered. >>>> >>>> >>> It's probaby better to use a short sliding window (of, say, 5 bp) and trim the ends until the window has no more than, say zero low quality base pairs. So, the following sequence would be converted from: >>> xxxoxooooooxxooooooxoxxx >>> to: >>> ooooooxxoooooo >>> >>> Florent >>> >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >>> >> >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-user >> > > > -- > Yanwei Tan > Institute of Neurobiology > 1.OG, AG Bading > Im Neuenheimer Feld 364 > University of Heidelberg > 69120 Heidelberg > Germany > > Tel:+49-6221-548319 > Fax:+49-6221-546700 >

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