Cucumber genome
by changlong wen
Hi,
In the NGS mapping option with "lastz" I cannot find the Cucumber genome.*
*Could you please make this reference genome available?
Or we have the reference sequence. How to add them in in the local server?
Many thanks.
Have a good day.
Best regards
changlong
9 years, 9 months
Cucumber genome
by changlong wen
Hi,
In the NGS mapping option with "lastz" I cannot find the Cucumber genome.*
*Could you please make this reference genome available? or we have the
reference sequence. How to add them in the list?
Many thanks.
Have a good day.
Best regards
changlong
9 years, 9 months
January 2012 Galaxy Events: Dec 15 Deadline for Czech Republic Workshop
by Dave Clements
Hello all,
The January Events <http://wiki.g2.bx.psu.edu/Events> email is going out a
little early this month, mainly because of a *December 15 deadline for
the Galaxy
Developer Workshop in the Czech
Republic<http://evomics.org/workshops/galaxy-developer-workshop/>
*.
There are Galaxy-related events on (at least) 3 continents next month:
* Date *
* Topic/Event *
* Venue/Location *
* Contact *
January 8-21
*2012 Workshop on
Genomics<http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-kru...>
*
Features Galaxy and much more.
Český Krumlov, Czech Republic
James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor>
January 14-18
*Galaxy Session<http://pag.confex.com/pag/xx/webprogrampreliminary/Paper2350.html>@
GMOD
Workshop<http://pag.confex.com/pag/xx/webprogrampreliminary/Session1123.html>
*, and
*The Galaxy Platform: Running Analyses in the
Cloud<http://pag.confex.com/pag/xx/webprogrampreliminary/Paper4623.html>@
Cloud
Computing Session<http://pag.confex.com/pag/xx/webprogrampreliminary/Session1139.html>
*
PAG 2012 <http://wiki.g2.bx.psu.edu/Events/PAG2012>, San Diego, California,
United States
Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements>
Dannon Baker
January 17
*Reproducible workflows for next generation sequencing
analysis<http://www.nowgen.org.uk/facilities/events/event.php?id=30>
*
Nowgen <http://www.nowgen.org.uk/>, University of
Manchester<http://www.manchester.ac.uk/>,
United Kingdom
Tom Hancocks <training(a)nowgen.org.uk>
January 23
*Galaxy Developer
Workshop<http://evomics.org/workshops/galaxy-developer-workshop/>
Application deadline is December 15.*
Český Krumlov, Czech Republic <http://www.ckrumlov.info/php/>, immediately
following the Workshop on
Genomics<http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-kru...>,
(which also features Galaxy content)
James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor>
January 26
*今回の講習会では，「Next-Generation Sequencer(NGS) 微生物解析と Galaxy
ツール」を中心に講義と実習を行ないます。講義内容をよりよく理解して 頂くために，PC
を使用した実習を行ないます。<http://www.ddbj.nig.ac.jp/ddbjing/ddbjing.html#DDBJ>
*
(Next-Generation Sequencing (NGS) and microbiological analysis with Galaxy)
DNA Data Bank of Japan (DDBJ), National Institute of
Genetics<http://www.ddbj.nig.ac.jp/>
DDBJ <http://www.ddbj.nig.ac.jp/addresses-j.html>
And I apologize in advance if I messed up the translation of the event at
DDBJ <http://www.ddbj.nig.ac.jp/ddbjing/ddbjing.html#DDBJ>!
Thanks,
Dave C.
--
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://galaxyproject.org/wiki/
9 years, 9 months
cufflinks-status-FAIL
by dongdong zhaoweiming
Hi,
I used the cufflinks to assemble my SAM file, but the results showed some CUFF's status in not "OK",it's FAIL, so that means these CUFF's corresponding sequence could not used or else mean? Thanks a lot!
Reards
weimin zhao
9 years, 9 months
GI error/shift in the output of megablast ?
by Sandrine Hughes
Dear all,
I have a trouble with the Megablast program available in NGS Mapping
and I hope that you can help. Indeed, I think that there might be a
problem with the table given in output, and notably a shift between
the GI numbers and the parameters associated.
Here are the details:
I. First, what I have done :
I used the program to identify the species that I have in a mix of
sequences by using the following options:
Database nt 27-Jun-2011
Word size 16
Identity 90.0
Cutoff 0.001
Filter out low complexity regions Yes
I run the analyses twice and obtained exactly the same results (I
used the online version of Galaxy, not a local one).
II. Second, I analysed the data obtained for one of my sequence
(1-202). The following lines are the beginning of the table that I
obtained after the megablast and two lines with troubles:
1-202 312182292 484 99.33 150 1 0 1
150 1 150 2e-75 289.0
1-202 312182201 476 99.33 150 1 0 1
150 1 150 2e-75 289.0
1-202 308228725 928 99.33 150 1 0 1
150 19 168 2e-75 289.0
1-202 308228711 938 99.33 150 1 0 1
150 22 171 2e-75 289.0
1-202 308197083 459 99.33 150 1 0 1
150 10 159 2e-75 289.0
1-202 300392378 920 99.33 150 1 0 1
150 10 159 2e-75 289.0
1-202 300392376 918 99.33 150 1 0 1
150 9 158 2e-75 289.0
1-202 300392375 922 99.33 150 1 0 1
150 11 160 2e-75 289.0
1-202 300392374 931 99.33 150 1 0 1
150 21 170 2e-75 289.0
1-202 300392373 909 99.33 150 1 0 1
150 21 170 2e-75 289.0
1-202 300392371 1172 99.33 150 1 0 1
150 9 158 2e-75 289.0
...
1-202 179366399 151762 98.67 150 2 0 1
150 46880 47029 6e-73 281.0
1-202 58617849 511 98.67 150 2 0 1
150 21 170 6e-73 281.0
III. Third, what I’ve noticed:
My first problem was that among all the species identified, two
were very different from the expected ones (2 last lines). So I
decided to search if that could be possible for this sequence and
performed independently a megablast on the NCBI with similar options.
I was not able to find these two species in the results.
So, I decided to check the hits identified in the table above and
identified a second problem. In the table, the second column give the
GI of the database hit and the third column give the length of the
database hit. However, when I manually checked in NCBI the length of
the GI, this one was incorrect. Indeed, for the GI 312182292, the
length should be 580 and not 484.
By checking different lines, I noticed that the length that is
given for a GI corresponds to the length of the GI-1. As you can see
in the above table, some GI are consecutive (300392376,
300392375,...). When checking the length of 300392376 in NCBI, I
should have 920. But when I checked 300392375, I found 918. And this
was true for the following lines : 300392374 give normally 922 and
300392373 give 931... My conclusion at that point was that there is a
shift of –1 between the GI and the other parameters of the line
(indeed the parameters for the remaining columns are in agreement with
the length of the GI-1). However, that’s not always true.... For some
GI given in the table (for example, the two last lines), if we check
the parameters of the GI-1, the parameters are completely different...
So, I suppose that there is a problem in the GI sorting during the
megablast but I’m not able to clearly define the problem.
IV. Fourth, confirmed with an other dataset
In order to be sure that the problem was not linked to my data or
my process, I asked a colleague to do a megablast on independent data.
The conclusions were similar to mine : a shift in the GI given in the
table and the parameters associated on the same line, that most of the
time but not always, correspond to GI-1.
Can you confirm that there is a problem with the output of the
megablast available in Galaxy ? If yes, do you think there is a way to
fix it ?
Thanks a lot,
Sandrine
9 years, 9 months
FASTQ Groomer before BWA mapping ?
by Praveen Raj Somarajan
All,
I'm wondering why do we need to convert Illumina FASTQ into sanger using FastQ Groomer before mapping with BWA in galaxy. The lastest version of BWA itself added -I option to use Illumina data directly. What's your opinion on this?
Secondly, I found that "Map with BWA for Illumina" uses -I option in the commandline during execution, even for sanger formatted reads. How does it impact the results?
Thanks,
Raj
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9 years, 9 months
TopHat
by Jennifer Jackson
Hello Tao,
The tools in the group "NGS: Picard (beta) -> QC/Metrics for sam/bam"
can generate statistics, in particular the tool SAM/BAM Alignment
Summary Metrics.
Another choice is "NGS: SAM Tools -> flagstat".
If more statistics are needed, then starting with the original FASTQ and
the mapping result SAM file, the tools in "Text Manipulation", "Filter
and Sort, and Join", and "Subtract and Group" can be used in custom
combinations.
This question was almost missed. I was able to locate, format, and send
as a new thread to the appropriate mailing list. Hopefully this reply
helps or you have already found the tools above.
Please help us to track new questions and provide prompt help by sending
tool and data questions:
1 - to either galaxy-user(a)bx.psu.edu or galaxy-dev(a)bx.psu.edu, which are
best for most questions. sending to galaxy-bugs(a)bx.psu.edu is mainly
reserved for UI bug reports (green bug icon for failed datasets) or for
sending shared links to private data.
http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions
2 - with the "to" as the mailing list address "galaxy-user(a)bx.psu.edu".
When a brand new question is sent with the mailing list as a "cc", it is
not tracked.
3 - when a new question is sent as a reply to an earlier thread with a
new subject line, it is not tracked. start a new thread for new
questions with new subject lines.
4 - please use "reply-all" if you would like more assistance about the
same subject to keep the thread consistent for the user community.
Thank you for your help with this!
Best,
Jen
Galaxy team
Peng, Tao wrote:
> Hi jen, after I did TopHat analysis of groomed FASTAQ data, how can I
> find information on how many total reads went into TopHat? How many
> reads were removed? How many unique hits to reference genome?
>
> I was trying to prepare a table for presentation and realize that I
> could NOT find the information in my GALAXY account?
>
> Thanks,
>
> tao
>
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
9 years, 9 months
Random Intervals ?
by Vincent Joseph Lynch
To Whom It May Concern,
I am curious if there is a tool within Galaxy to generate a set of random intervals from a particular genome similar to the "Random Intervals" tool within the ENCODE tools? I am using the "Aggregate datapoints" tool to get phastCons conservation scores for peaks from ChIP-Seq data. I would like to compare these scores to a random expectation so would like to be able to use a Random Intervals-like tool to generate a set of random positions to compare to the experimental set.
Best,
Vinny
Vincent J. Lynch, Associate Research Scientist
Department of Ecology and Evolutionary Biology & Yale Systems Biology Institute
Yale University
"There is a grandeur in this view of life, with its several powers,
having been originally breathed into a few forms or into one; and that
whilst this planet has gone on cycling according to the fixed laws of
gravity, from so simple a beginning endless forms most beautiful and most
wonderful have been, and are being, evolved." -C. Darwin, 1859
9 years, 9 months
Question re: Quota not re-setting after data deletion
by Mcgowen, Michael
Hello,
I'm using the Galaxy Main --I was trying to groom data that I had uploaded at about 11 AM EST and Galaxy informed me that I had met my quota. Indeed it said that my quota was 98% full, but my history (my only one) said that I had about 13 Gb-- I deleted everything in my history in order to start fresh, but it still keeps saying my disk is 98% full every though my history has 0 bytes. At the moment, I have nothing in my history, but it is still saying my disk is 98% full. How do I reset the quota to 0 if not by deleting data?
Michael R. McGowen, Ph.D.
Postdoctoral Research Fellow
Molecular Evolution Laboratory
Center for Molecular Medicine and Genetics
Wayne State University School of Medicine
3240 Scott Hall
540 E. Canfield St.
Detroit, MI 48201 USA
313-577-0086
mmcgowen(a)med.wayne.edu
http://homopan.wayne.edu/people/mmcgowen.html
9 years, 9 months
