May 2011 - galaxy-user - lists.galaxyproject.org

Indel work flow questions
by Mike Dufault 03 May '11

03 May '11

Hi All, I have a question about the NGS: Indel analysis and SNP Calling. Assuming I have loaded my paired end reads, groomed, and got all the way through to alignment with BWA my question the becomes does the analysis for indel analysis and SNP analysis split in the work flow? For SNP analysis, It seems that I need to filter on SAM, convert SAM-to-BAM, etc... For Indel, It seem that I should use the BWA output that is in SAM format for indel analysis. Are these two above statments correct? I also have a question regarding the input for indel analysis. Should I use the BWA output directly (which is in SAM format) or should I first "filter on SAM" and use that output (which is also in SAM format). I have tried the indel analysis using both filtered and unfilterd and I get very similar results. It seems to me that should use the "filtered on SAM" output where I can indicate that the reads are paired=Yes, proper pairs=yes, unmapped=NO. Any thought, insight, etc. Thanks if advance, Mike

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RNA seq analysis
by puvan001＠umn.edu 03 May '11

03 May '11

I am new to Galaxy and I am not sure whether these topics were discussed earlier. I followed the steps up to cufflinks and I did not have any problems. Thanks for the RNA seq tutorial. My questions are 1. How do I know the number of reads mapped against the reference genome used after Top Hat mapping 2. I am aware that Cuffdiff is used to find the differences in expression. How do I combine replicates (3) of different treatments ? SP

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quality stat.
by Robin Mjelle 03 May '11

03 May '11

Dear User, I am trying to use the tool "Compute quality statistics<http://main.g2.bx.psu.edu/tool_runner?tool_id=cshl_fastx_quality_statistics>" in galaxy on Ilumina single reads. The file is 2.3 Gb, fastq format. I have performed Quality format converter on the data set and the format is now qualillumina. Despite of this, galaxy don't recognize any dataset in the workflow to use as input into quality statistics. Any idea why my dataset is not accepted as input? Best, Robin

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change queue with sge
by Sylvain Thomas 03 May '11

03 May '11

Hi I currently use a galaxy server with cluster. This cluster uses SGE. I'd like to specify a queue other than the default. I have tried many combinaisons with drmaa:/// without success. The queue used is always the default one. Does anyone has solved this problem? Thanks, Sylvain -- Sylvain Thomas tel : +33 (0)5 61 28 54 27 INRA - Unité de BIA Génopôle - plateforme Bio-informatique Chemin de Borde-Rouge - AUZEVILLE BP 52627 - 31326 CASTANET-TOLOSAN CEDEX

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uploading files from remote server
by camelia botez 02 May '11

02 May '11

How can we upload files from remote server running galaxy and using big storage for data ? Thank you

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Only first 5000 reads are displayed in this tile
by Jeremy Chien 02 May '11

02 May '11

Hi During the visualization of my mRNAseq data, some area have red line indicating that only the first 5000 reads are displayed. Within this region, some area have many reads. Some area, where exons exist, I don't see any reads. How do I interpret the data? If there are no reads shown in the visualization, although there is a read line saying only the first 5000 reads are displayed, does the absence of reads corresponding to a particular exon means it is not expressed? Thanks, Jeremy

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runtime warning with pysam egg
by Shantanu Pavgi 02 May '11

02 May '11

Hi, I am getting following warning when I start the galaxy server. I am using latest revision (50e249442c5a) of galaxy-dist. Am I missing anything in the configuration here? {{{ $ ./run.sh /home/galaxy/.python-eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg-tmp/csamtools.so:6: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility ###t#|}#######b###############S#5#####D###i)#######[####x,m ###<#=####L########B###########q##.:######$2###rDM###E3A#########j### python path is: /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/numpy-1.3.0-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Whoosh-0.3.18-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/bx_python-0.7.0_14b6a6c95da6-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/amqplib-0.6.1-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pexpect-2.4-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Babel-0.9.4-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Beaker-1.4-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Mako-0.2.5-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/WebHelpers-0.2-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/wchartype-0.1-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/elementtree-1.2.6_20050316-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/docutils-0.7-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/WebOb-0.8.5-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Routes-1.12.3-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/PasteDeploy-1.3.3-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/PasteScript-1.7.3-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Paste-1.6-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/lib, /share/apps/galaxy/python/2.6.6/lib/python26.zip, /share/apps/galaxy/python/2.6.6/lib/python2.6, /share/apps/galaxy/python/2.6.6/lib/python2.6/plat-linux2, /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-tk, /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-old, /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-dynload, /share/apps/galaxy/python/2.6.6/lib/python2.6/site-packages galaxy.datatypes.registry DEBUG 2011-04-25 12:37:54,637 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2011-04-25 12:37:54,650 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False ... ... ... }}} -- Thanks, Shantanu.

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Removing deleted datasets
by Simon Lank 02 May '11

02 May '11

Hi. Our current galaxy database is ~ 600 gb, most of which are user deleted datasets. I followed the instructions here: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDa… and ran the shell scripts in recommended order. One of them in particular (I think it was purge_histories.sh) took amost 24 hours to complete. However, it doesn't appear any / most of the files were actually deleted, since we still have ~ 600 gb of dataset files. Is there something obvious I can try to get the files purged correctly? Thanks. Simon Simon Lank Research Specialist O'Connor Lab, WNPRC 555 Science Dr. Madison WI (608) 265-3389

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