CEAS in Galaxy
by shamsher jagat
Is there an option of running CEAS tool in Galaxy I want to annotate
selected enriched regions of ChIP seq data with gene names etc?
Thanks
10 years, 7 months
fastq joiner problem
by Matthew Herron
Hi,
I am trying to join two groomed fastq files from a paired-end Illumina
read using the fastq joiner tool. The drop-down menus correctly
identify the groomed fastq files, but after cranking for a few minutes
the tool produces empty output:
"FASTQ joiner on data 5 and data 4emptyformat: fastqsanger, database:
?Info: There were 3497909 known sequence reads not utilized.Joined 0
of 3497909 read pairs (0.00%)."
The files have the same number of reads (3497909), reads have the same
number of bases (102), and the joiner tool doesn't have any options
(other than choosing the two files to join). I have tried this with
Sanger and with Illumina 1.3+ quality scores, and in both (left-right)
orientations. I've pasted the beginnings of the two files below my
signature in case this is useful for diagnosing the problem.
Can anyone tell me what I'm doing wrong? Thanks,
--
Matthew D. Herron, PhD
Department of Zoology
University of British Columbia
X.princeps(a)gmail.com
http://www.eebweb.arizona.edu/grads/mherron/
Sample of read 1:
@HWI-ST765:83:D091AACXX:1:1101:1202:2130 1:N:0:ACTTGA
TTATTCCGTTTACCTTCACGCTGTTATGGCTCTCGGTGTTCGGCAATAGCGCGCTGTATGAAATTATCCACGGCGGCGCGGCATTTGCCGAGGAAGCGATG
+
CCCFFFFFHHHHHJJJJJJJJJJJJIJIJJJIEHII?FGIIJJJJJJJIJJJHFFDDEEEDEDDDDEDDDDDDDDDDDDDDDDDDD@CCD3<BDD@DDDBD
Sample of read 2:
@HWI-ST765:83:D091AACXX:1:1101:1202:2130 2:N:0:ACTTGA
ATTCCCCAGCACCAGCGCCCCGGAGTCCGCCGAGGTCACATAAAACAGCAGGCCAGTAATGGTGGCGACGGAGGCGCTAAAGGTAAACGCCGGATACTGCG
+
CCCFFFFFFGHHHJJJJJJJJJIJIFHIIJJJJIG:BEFFFFEEEDDCBDDDDDDD@CDDDCACDDDBDDDDDDBDDDDDDDC>@CCC@@DDDDDDDDEDB
10 years, 8 months
adaptor trimming
by Soetkin Versteyhe
Hi!
Does anyone know if it is possible to trim sequencing adaptor sequences away in Galaxy?
Thanks!
Soetkin Versteyhe, PhD
PostDoc
University of Copenhagen
Faculty of Health Sciences
The Novo Nordisk Foundation
Center for Basic Metabolic Research
Integrative Physiology
Blegdamsvej 3B
2200 København N
Denmark
PHONE +45 35337116
soetkin.versteyhe(a)sund.ku.dk
http://sund.ku.dk
http://metabol.ku.dk<http://metabol.ku.dk/>
[cid:image001.gif@01CC9E39.FE2E3F70]
10 years, 8 months
Data gets deleted from public server
by shamsher jagat
I uploaded two BAM files and was working with them but when I tried to use
them again they are automatically deleted along with all the steps
of analysis?
Any reason or I am missing something.
Shamsher
10 years, 8 months
Cufflink error
by Lizex Husselmann
Hi
I've started an alignment using the command line (Tophat v1.3.3). I've uploaded the files (accepted.bam) onto Galaxy and upon doing the Cufflinks analysis on the Galaxy interface, it shows an error. I had to look at the options. I've change the options to default and run it again but still the same error. Is the accepted.bam file not compatible with the Galaxy Cufflinks? Is there something I not doing?
Kind regards
Lizex
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10 years, 8 months
SNPeff tool?
by Laura Elizabeth Spoor
Hi,
I use the Galaxy server and was wondering how to use SNPeff tool? I
have seen that it can be integrating with Galaxy on their website
(http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot
see it on the server? Is it something that can be run on the server?
Best Wishes,
Laura
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
10 years, 8 months
Cuffcompare error
by Alessia D
Hi,
I am trying to run Cuffcompare on a set of 6 Cufflinks-generated datasets
(3 replicates of 2 conditions). I am consistently getting the following
error:
Error running cuffcompare. Warning: Your version of Cufflinks is not
up-to-date. It is recommended that you upgrade to Cufflinks v1.1.0 to
benefit from the most recent features and bug fixes
(http://cufflinks.cbcb.umd.edu).
Error: no XLocus created for transcript CUFF.34072.1 (file ./input3)
[2, 2], on chrY+:274296-277218
However, if I run Cuffcompare on the 2 conditions separately (3x Cufflinks
datasets), everything works fine.
Does anyone know why this is?
Thanks
Alessia
10 years, 8 months
Uploading Genome from Ensembl
by Scroggins, Sheena
How do I upload the Zebrafish genome from Ensembl to my user history in Galaxy? I'm trying to map my RNA-Seq data using TopHat and need to map it to the Ensembl version of ZFv9, but Galaxy only has the UCSC version built in. The Ensembl version is slightly different.
Thanks,
Sheena
10 years, 8 months
number of concurrent jobs/user
by Petr Novak
Is it possible to limit number of concurrent jobs when job_runner is pbs?
The setting in universe_wsgi.ini is obviously limiting only locally run
jobs.
Petr
10 years, 8 months
