I am a new user of galaxy. i met a problem and didnot find similar
question in FAQ. I wanted to upload the data from DDBJ DRA dataset to
galaxy through UTL method. The file is around 800M. However after
uploading, the FASTQ file was just around 2M. So I wanted know whether
it is possible to upload a large file to galaxy through URL method? or
I should download the file to my pc and then uploading to galaxy
through FTP method.
Hello, I tried to search in the forums and although this question has appeared many times I still don't have a solution.
I cannot manage to upload big files into the local galaxy, it just takes ages. Can I not just copy and paste into a local directory? why do I have to upload the files if it is already installed locally?
I do not have a server webpage in order to use the url address option
If I do it through ftp (locally) what ftp address shall I put? ftp localhost:8080??
Is there any other option to speed up uploading, is so slow that is no longer worth using it, please help me!
Is there a more detailed explanation on what "Find Diagnostic hits" module in Metagenomic analysis does? Does it take all the hits above user specified cutoffs to one query and return the taxon name if and only if all the hits have the same taxon (my understanding)? Or, does it look at the top few hits or??? Thanks for providing some clarification on the method.
Thanks for pointing out this issue.
The BLAST databases we have on Galaxy are from last year, while those on
NCBI website are the latest (Jan 2012). As pointed out on NCBI website (
http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html), it appears that each
time any change is made to a sequence/database, GI numbers change as well.
This is perhaps why you're observing discrepancies in GI numbers and
lengths between megablast outputs on Galaxy and NCBI. I'm currently in the
process of downloading the latest BLAST databases from NCBI, and I'll let
you know when they're available for use on Galaxy.
Thanks for your patience,
On Wed, Nov 9, 2011 at 8:03 AM, Sandrine Hughes <Sandrine.Hughes(a)ens-lyon.fr
> Dear all,
> I’m not sure where I need to send my email so I apologize if I’m wrong.
> 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 trouble 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 that 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 trouble. 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
> 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 was 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 trouble 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, 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 you can fix it ?
> Many thanks for your help,
> Best regards,
Graduate student, Bioinformatics and Genomics
Makova lab/Galaxy team
Penn State University
505 Wartik lab
University Park PA 16802
The BAM/SAM files can be visualized in Trackster, using your custom
reference genome (the same dataset as used for Bowtie or TopHat). But,
there are no Cufflinks results, and therefore nothing to visualize, due
to the parameters used.
Since you are working with a bacterial genome, the parameters will need
to be tuned to account for the lack of transcript splicing. The best
resources for advice are likely seqanswers or the tool authors, as
explained in this prior answer to another bacterial genome/RNA-seq question:
Recently, there has been some user discussion about RNA-seq analysis and
bacterial genomes on the galaxy-user mailing list. If you want to search
and read through the Q&A, using our custom google search is the best way
to locate the threads (but, expect to find just a few):
If anyone else reading this thread has help to offer, please feel free
to jump in and share any working knowledge for this type of analysis.
Best wishes for your project,
On 2/29/12 12:31 PM, Ateequr Rehman wrote:
> hello Jennifer
> Thanks a lot, here is the link
> *From:* Jennifer Jackson <jen(a)bx.psu.edu>
> *To:* Ateequr Rehman <ateeqrr(a)yahoo.com>
> *Cc:* "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu>
> *Sent:* Wednesday, February 29, 2012 9:24 PM
> *Subject:* Re: [galaxy-user] Visualise data
> Hi Ateeq,
> Please share a link to your history so that we can provide feedback. Use
> "Options -> Share or Publish", generate the share link (first button),
> copy the link into a reply email, and send that back to me directly.
> Also, your last few questions have been sent as replies to other
> questions on the mailing list with a new subject line. This causes them
> to thread/track incorrectly (and potentially be missed). When sending a
> new question, please start with a brand new message, address the "to" as
> "galaxy-user(a)bx.psu.edu <mailto:firstname.lastname@example.org>" and this will
> reach us correctly.
> Thank you and I will watch for your reply,
> Galaxy team
> On 2/29/12 11:30 AM, Ateequr Rehman wrote:
> > Hello Admin and users
> > i wanted to visualize my data, i ran Tophat and converted sam to BAM and
> > then cufflink,
> > but totally unable to see any output data,
> > any suggestion, how i could see my results
> > For administrators, on my account run number 76 to 79 are the run i want
> > to visualize
> > Thanks
> > Ateeq
> > ___________________________________________________________
> > The Galaxy User list should be used for the discussion of
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> Jennifer Jackson
I am starting off with 454 read data in an sff file. I would like to get
quality statistics on the data, but having trouble getting the tools to
I first tried to convert to a fastq file and use the "Compute Quality
Statistics" tool, but I get this error, "An error occurred running this job:
*fastx_quality_stats: found invalid nucleotide sequence "*
I then tried the "fastq groomer" and repeated the "Compute Quality
Statistics", but got the same error. Perhaps it cannot handle the longer
Alternatively I tried converting the sff file to a fasta file and quality
file. I had to manually convert the quality data file to qual454 for the
"Build Base Quality Distribution" tool to recognize it, but upon doing that
I got this error: *"*An error occurred setting the metadata for this
dataset." And the Build Base Quality Distribution tool, also failed.
Any help resolving this issue would be appreciated,
I would like to add some filtering steps in my RNA-Seq pipeline. To do so,
I used the accepted.hits from TopHat and apply a filter using NGS: SAM
Tools > Filter SAM and select reads with bitwise flag 0x0002. This does the
job. However, I am unable to use cufflink after this step and got the
following error message that seems to indicate that the file contains no
header and is unsorted. Is there a workaround ?
Thanks a lot
Error running cufflinks.
return code = 1
cufflinks: /lib64/libz.so.1: no version information available (required by
cufflinks -q --no-update-check -s 20 -I 300000 -F 0.100000 -j 0.150000 -p 8
-m 200 -g /galaxy/main_pool/pool5/files/003/858/dataset_3858145.dat
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File /galaxy/main_pool/pool1/files/003/858/dataset_3858306.dat doesn't
appear to be a valid BAM file, trying SAM...
[14:11:28] Loading reference annotation.
[14:11:28] Inspecting reads and determining fragment length distribution.
Error: this SAM file doesn't appear to be correctly sorted!
current hit is at chr10:181061, last one was at chr1:245006405
Cufflinks requires that if your file has SQ records in
the SAM header that they appear in the same order as the chromosomes names
in the alignments.
If there are no SQ records in the header, or if the header is missing,
the alignments must be sorted lexicographically by chromsome
name and by position.
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I used FASTQ groomer on a 29 Gb Illumina 1.5+ FASTQ file to go from
Illumina 1.3-1.7+ to Sanger and it is still processing after over 30
hrs. Is this a normal time frame for a FASTQ file this size ?
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