Deleted history
by Herve Rhinn
Hi,
I have not been using Galaxy for a few months an it seems that a least
one of my history was deleted.
I assume it is because of inactivity for too long/exceeding the new quotas.
Would there be by chance a a way to re-access it temporarily to be able
to download some of that data or has it been totally erased?
Thanks lot,
Herve Rhinn
9 years
Re: [galaxy-user] Names for genes in RNA-Seq analysis (Emilie Chautard)
by Emilie Chautard
Hi Olivier,
Did you try to run Cuffcompare (part of Cufflinks) on your results?
According to the Cufflinks manual (http://cufflinks.cbcb.umd.edu/manual.html
):
>Cufflinks includes a program that you can use to help analyze the
transfrags you assemble. The program cuffcompare helps you:
> - Compare your assembled transcripts to a reference annotation
> [...]
In the Galaxy version of Cuffcompare, I think that you can provide a
reference annotation file using "Use Reference Annotation:", which will be
compared to your results with Cufflinks.
It makes an "union" of the transcripts obtained with Cufflinks with the
annotation file (both in *.gtf format). You can then obtain a transcript
identifier for those already annotated.
It also provides a class code for the transcripts, which can inform about a
potential isoform for example.
Hope this helps.
Emilie
--
Emilie Chautard, PhD
Postdoctoral Fellow
Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
Tel: 416-673-8518
Toll-free: 1-866-678-6427
www.oicr.on.ca
> Message: 7
> Date: Thu, 20 Oct 2011 15:12:45 +0200
> From: GANDRILLON OLIVIER <olivier.gandrillon(a)univ-lyon1.fr>
> To: "galaxy-user(a)bx.psu.edu" <galaxy-user(a)bx.psu.edu>
> Subject: [galaxy-user] Names for genes in RNA-Seq analysis
> Message-ID: <CAC5EAED.8E99%olivier.gandrillon(a)univ-lyon1.fr>
> Content-Type: text/plain; charset="windows-1252"
>
> Hello
>
> I am using Galaxy to analyse RNA-seq libraries made from chicken cells.
>
> I just groomed my sequences, passed them through TopHat and then Cufflinks.
>
> This worked well and in the end I get a list of genes and their respective
> FPKM values.
>
> My only problem is that the names of the genes do not appears in the
> listing, they are simply reference as "CUFF.1, CUFF.2, " etc?
>
> Could you please tell me how I could obtain gene names? (I went through the
> FAQ and could not get the answer).
>
> Sincerely
>
> Olivier
>
9 years, 1 month
cufflinks error
by jh yu
Dear all:
Recently I am using cufflinks to analyze differential expression between different conditions, but when using cufflinks an error occurred:
An error occurred running this job:cufflinks v1.0.3
cufflinks -q --no-update-check -I 1 -F 0.050000 -j 0.050000 -p 8 -g /galaxy/main_database/files/002/991/dataset_2991920.dat
Error running cufflinks. [bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this
However, when I used the same parameters to analyze another file, it worked well:
19,904 lines
format: gtf, database: rhodRHA1
Info: cufflinks v1.0.3
cufflinks -q --no-update-check -I 1 -F 0.050000 -j 0.050000 -p 8 -g /galaxy/main_database/files/002/991/dataset_2991920.dat
The only difference is the size of each file, the failed one input file is 23 G, while the succeeded one input file is 3.5 G, is the size causing failure?
Thank you in advance.
Best wishes!
Sincerely, Jinhai YU
Jinhai YU, Ph.D Candidate
010-64888521
Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
9 years, 2 months
cufflinks set parameters
by dongdong zhaoweiming
Hi,
It's the first time for me to use cufflinks in galaxy, two choices confused me as follows:
Perform Bias Correction:
No Yes
Bias detection and correction can significantly improve accuracy of transcript abundance estimates.
Set Parameters for Paired-end Reads? (not recommended):
No Yes
what is the Bias correction and how does it work? And for "set parameters for paired-end reads? (not recommended)" ,what would be important difference between recommended and not recommended?
Thanks a lot!
dongdong
9 years, 2 months
data format
by Klaudyna Borewicz
Hi,
I would like to use Galaxy to run LEfSe, but I don't know how to get
the data into tabular format that is required
(http://huttenhower.org/galaxy/tool_runner?tool_id=LEfSe_for). My data
is 454 fasta files that I was analyzing with RDP to get the
classification. It works fine, I get .txt file that i can load to
Galaxy, it looks like this:
norank Root 37646
unclassified_Root 9
domain Bacteria 37637
unclassified_Bacteria 5998
phylum OD1 0
unclassified_OD1 0
genus OD1_genera_incertae_sedis 0
phylum BRC1 0
unclassified_BRC1 0
genus BRC1_genera_incertae_sedis 0
phylum Deferribacteres 0
unclassified_"Deferribacteres" 0
class Deferribacteres 0
unclassified_Deferribacteres 0
order Deferribacterales 0
unclassified_Deferribacterales 0
family Deferribacterales_incertae_sedis 0
unclassified_Deferribacterales_incertae_sedis 0
genus Caldithrix 0
family Deferribacteraceae 0
unclassified_Deferribacteraceae 0
genus Calditerrivibrio 0
genus Mucispirillum 0
.....
but i need to have the labels in a hierarchical organization and I
cannot find the way to get it to work. Please let me know if you have
any suggestions, or maybe RDP is just not the way to go.
Thank you and hope to hear from you soon,
Klaudyna
--
____________________________________________________
Klaudyna Borewicz M.Sc, B.Sc
Department of Veterinary and Biomedical Sciences
University of Minnesota
1971 Commonwealth Ave.
St. Paul, Minnesota 55108
Phone: (612)624-6226
FAX: (612)625-5203
9 years, 2 months
Downloading files
by KNIGHT M.R.
Is there any way of downloading processed files by e.g. FTP, rather than
"Save as" in the web browser? I have a large (9.6Gb) BAM file to
download, and downloading it via the browser seems unstable for some
reason. Thanks, Marc.
9 years, 2 months
Removing low quality reads
by Getiria Onsongo
Galaxy Users,
I would like to filter a .bam file to remove reads with low mapping quality,
especially ambiguously mapped reads (MAPQ = 0). I can easily do this using
the command line version of samtools as shown below.
samtools view -bq 20 hba1.bam > hba1_MAPQ20.bam
None of the options available under "NGS:SAM Tools" (e.g., Generate pileup
and Filter SAM) provide an option for removing reads with low mapping
quality. The history shown in
http://main.g2.bx.psu.edu/u/onsongo/h/obtaininghighqualityreads
shows the results I would like to obtain.
Data 2 shows the results of Picard tools SAM/BAM Alignment Summary
Metrics<http://main.g2.bx.psu.edu/tool_runner?tool_id=PicardASMetrics>
on
hba1.bam which contains reads with MAPQ values less than 20. As shown in
this summary html, PF_READS_ALIGNED = 775 and PF_HQ_ALIGNED_READS = 241.
Data 4 shows the results of Picard tools SAM/BAM Alignment Summary
Metrics<http://main.g2.bx.psu.edu/tool_runner?tool_id=PicardASMetrics>
on hba1_MAPQ20.bam which contains only reads with MAPQ greater than or
equal to 20. As shown in this summary html, PF_READS_ALIGNED = 241 and
PF_HQ_ALIGNED_READS = 241.
Is there a way in Galaxy to filter a bam file to remove low quality mapped
reads similar to using the samtools command line alternative shown above?
Thanks,
Getiria
--
Getiria Onsongo, Ph.D.
Bioinformatics Research Scientist
Masonic Cancer Center,
University of Minnesota
Minneapolis, MN 55455
Phone: 612-625-0101
9 years, 2 months
Re: [galaxy-user] Names for genes in RNA-Seq analysis
by Jennifer Jackson
Hello Olivier,
When deleting data, it takes the server a short amount of time to
refresh. It may take a bit longer right now since many people are
performing this action at the same time.
For the RNA-seq analysis question, reference annotation GTF files are
used by the Cuff* programs. (These are different than the result GTF
files produced by the programs). For reference annotation GTF files,
there are many sources, including Ensembl and UCSC. Here are links to a
tutorial and an FAQ that can help with your usage question.
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq
But, there are many small details to running the tools to get the
optimal results. These types of questions concerning functionality are
best directed to the tool authors at tophat.cufflinks(a)gmail.com
Take care,
Jen
Galaxy team
On 10/25/11 11:24 PM, GANDRILLON OLIVIER wrote:
> Hello Jennifer
>
>
> Le 26/10/11 02:15, « Jennifer Jackson »<jen(a)bx.psu.edu> a écrit :
>
>> Hello Olivier,
>>
>> Are you using a reference gene annotation GTF file?
>
> Well if I do , I do not know :-)
>
> What I used is first TopHat and then Cufflink. At what stage shall I use
> such a GTF file?
> And additionnaly: where shall I find such a GTF file?
>
> As I understand it: there are tow sources for a GTF file:
> 1. The output from cufflinks generates one (but there is no gene names in
> it..)
> 2. I could get one from Ensembl?
>
> Shall I then use Cuffcompare on the cufflink output?
>
> Best
>
> Olivier
>
> PS: I am now stuck with the galaxy websute that state that I am over my
> disk quota. I have deleted a couple of files but this does not seems to
> help...
>
>
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
9 years, 2 months
