galaxy-user April 2013

galaxy-user@lists.galaxyproject.org

45 participants
63 discussions

Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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SNP finding
by Xiefan Fang 03 Dec '13

03 Dec '13

Dear galaxy users, We have done deep sequencing on some known genomic loci using Hiseq2000. I have already mapped the reads to the reference sequences by using Galaxy. In the next step, I want to find SNPs and calculate the SNP percentage within the reads. There are 500,000 to 1,000,000 reads per biological sample. Can I do it with galaxy? If not, is there other programs available in windows? Considering that I am not very familiar with programming. Thanks, Xiefan University of Florida

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analysing pooled data with FreeBayes
by Nicola Smith 24 Jul '13

24 Jul '13

Hi, I am new to this and I hope someone can help. I have pooled sequencing data that I am trying to analyse using Galaxy. I've done quite a bit of online searching and it seems that FreeBayes should be able to do this, if I select "set population", click the "Assume that samples result from pooled sequencing" option and change the ploidy to nx2 (number of alleles, where n is the number of subjects and the organism is diploid). However, whenever I do this I get an error: usually just "Killed" I was originally setting my polidy rather high (190 as I have 95 subjects pooled), so I wondered if this was the problem, however, it fails if I do a ploidy of only 4 too. I've tried various things to try to see where I am going wrong: All with the same BAM file: Set population model options: Do not set --> works Set population model options: set, Assume that samples result from pooled sequencing: not ticked, Default ploidy for the analysis: 2 --> works Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 2 --> works Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 4 --> fails (killed) Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 10 --> fails (killed) Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 10 --> fails (killed) It seems that it is the ploidy part that I am doing wrong, as it works with pooled data but ploidy of 2. I'm sure I have to change the ploidy though, or else how does the program know how many subjects are in the pool? Also, everywhere that I've ready says you have to change the ploidy. I apologise if my question is naive. As I said, I am new to Galaxy and this is the first thing I am trying to do! Any help / suggestions would be appreciated, Thanks, Nic

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barcode splitter files web based
by Ann Holtz-Morris, M.S. 11 Jul '13

11 Jul '13

HI, I'm trying to use the output files from barcode splitter. I know that the command line as some wrappers made that take the output files and puts them in the history. Is there anything similar for output files but for us biologists who don't do command line? J Thanks, Ann CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

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List of genomes
by YBao 01 Jun '13

01 Jun '13

Hi All, I was trying to map a set of data to a genome, Klebsiella pneumoniae subsp. Pneumoniae MGH 78578(31). While uploading the reads, I was able to find the reference genome as listed above. However, when I tried to map the data using wither bowtie or BWA, the pull down list did not include this genome. Can someone help or enlighten me as why it did not make into the list? Thanks Yongde -- Yongde Bao DNA Sciences Core Dept. of Microbiology, Immunology, and Cancer Biology UVA

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Map with BWA for Illumina is hung
by Casey,Richard 13 May '13

13 May '13

Hi, when we try using Map with BWA for Illumina on the public server, it never starts running and sits in a queued state forever. We have jobs that have been queued for more than 5 days. Any ideas on why these jobs never start? ------------------------------------------- Richard Casey, PhD CSU 970-492-4127 970-980-5975 richard.casey(a)colostate.edu<mailto:richard.casey@colostate.edu>

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Tophat for Illumina is not running
by lilach noy 01 May '13

01 May '13

Hello, I'm new to Galaxy so I think i'm at the right place asking this, though please let me know if I got it all wrong. I sent a Tophat query on Thursday about 5 days ago and it is still waiting to ran (gray background). Is to O.k? A bug? Should i keep waiting or stop everything and restart? If this is not the address for reporting a suspicious bug, whom does this concern? Thank you very much, Lilach

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Can Galaxy help with Comparative Genomics?
by Joshua Burkhart [uoregon.edu] 30 Apr '13

30 Apr '13

The lab I work with would like to compare a few populations' genomes of a species with an unpublished genome assembly. I have sequence data for each population that was created using only single-size insertion sequences, yielding only short paired-end reads. I was able to create a genome assembly for one of the populations and would like to see how it compares to another closely related species (which has a published genome). I used Augustus (http://bioinf.uni-greifswald.de/augustus/) to produce a GFF annotation for my assembly but am not sure how to best go about comparing my assembly to the published assembly of the other species. Can Galaxy help? Are there other tools that may be of use? I tried using ACT (http://www.sanger.ac.uk/resources/software/act/) but it never finished. These genomes are approximately 1Gbp. Any advice would help. Thanks, Joshua Burkhart

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GFF parsing with biopython
by Mic 30 Apr '13

30 Apr '13

Hi, I have the following GFF file from a SNAP X1 SNAP Einit 2579 2712 -3.221 + . X1-snap.1 X1 SNAP Exon 2813 2945 4.836 + . X1-snap.1 X1 SNAP Eterm 3013 3033 10.467 + . X1-snap.1 X1 SNAP Esngl 3457 3702 -17.856 + . X1-snap.2 X1 SNAP Einit 4901 4974 -4.954 + . X1-snap.3 X1 SNAP Eterm 5021 5150 14.231 + . X1-snap.3 X1 SNAP Einit 6245 7325 -1.525 - . X1-snap.4 X1 SNAP Eterm 5974 6008 5.398 - . X1-snap.4 With the code below I have tried to parse the above GFF file from BCBio import GFF from pprint import pprint from BCBio.GFF import GFFExaminer def retrieve_pred_genes_data(): with open("test/X1_small.snap.gff") as sf: #examiner = GFFExaminer() #pprint(examiner.available_limits(sf)) for rec in GFF.parse(sf): pprint(rec.id) pprint(rec.description) pprint(rec.name) pprint(rec.features) #pprint(rec.type) #'SeqRecord' object has no attribute #pprint(rec.ref) #'SeqRecord' object has no attribute #pprint(rec.ref_db) #'SeqRecord' object has no attribute #pprint(rec.location) #'SeqRecord' object has no attribute #pprint(rec.location_operator) #'SeqRecord' object has no attribute #pprint(rec.strand) #'SeqRecord' object has no attribute #pprint(rec.sub_features) #'SeqRecord' object has no attribute retrieve_pred_genes_data() and got the following output: 'X1' '<unknown description>' '<unknown name>' [SeqFeature(FeatureLocation(ExactPosition(2578), ExactPosition(2712), strand=1), type='Einit'), SeqFeature(FeatureLocation(ExactPosition(2812), ExactPosition(2945), strand=1), type='Exon'), SeqFeature(FeatureLocation(ExactPosition(3012), ExactPosition(3033), strand=1), type='Eterm'), SeqFeature(FeatureLocation(ExactPosition(3456), ExactPosition(3702), strand=1), type='Esngl'), SeqFeature(FeatureLocation(ExactPosition(4900), ExactPosition(4974), strand=1), type='Einit'), SeqFeature(FeatureLocation(ExactPosition(5020), ExactPosition(5150), strand=1), type='Eterm'), SeqFeature(FeatureLocation(ExactPosition(6160), ExactPosition(7325), strand=-1), type='Einit'), SeqFeature(FeatureLocation(ExactPosition(5973), ExactPosition(6008), strand=-1), type='Eterm')] and with GFFExaminer I got these: {'gff_id': {('X1',): 8}, 'gff_source': {('SNAP',): 8}, 'gff_source_type': {('SNAP', 'Einit'): 3, ('SNAP', 'Esngl'): 1, ('SNAP', 'Eterm'): 3, ('SNAP', 'Exon'): 1}, 'gff_type': {('Einit',): 3, ('Esngl',): 1, ('Eterm',): 3, ('Exon',): 1}} I found these examples ( https://github.com/patena/jonikaslab-mutant-pools/blob/master/notes_on_GFF_…), but I got these kind of errors: #pprint(rec.type) #'SeqRecord' object has no attribute #pprint(rec.ref) #'SeqRecord' object has no attribute #pprint(rec.ref_db) #'SeqRecord' object has no attribute #pprint(rec.location) #'SeqRecord' object has no attribute #pprint(rec.location_operator) #'SeqRecord' object has no attribute #pprint(rec.strand) #'SeqRecord' object has no attribute #pprint(rec.sub_features) #'SeqRecord' object has no attribute What did I do wrong and how is it possible to access all fields in the above GFF file? Thank you in advance. Mic

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Re: [galaxy-user] GenBank database files
by Peter Cock 29 Apr '13

29 Apr '13

On Mon, Apr 29, 2013 at 3:27 AM, Mike Dyall-Smith <mike.dyallsmith(a)gmail.com> wrote: > Dear Peter Cock, thanks for your advice. Just to be clear, do I leave the > files within their decompressed folders or do I put all the individual files > into one folder? I assume the former, but want to be sure. > Thanks again, Mike DS Hi Mike, Unless you're using a Graphical decompression tool which is trying to be too helpful, each tar-ball does *not* decompress into its own folder. The files should all be in the *same* folder. I use this to verify the checksums, $ md5sum --check nr.00.tar.gz.md5 nr.00.tar.gz: OK Then I use this to decompress the tar-balls, $ tar -zxvf nr.00.tar.gz etc (Actually I don't do this personally any more - it has been setup to happen automatically when the NCBI update the databases.) We keep all our NCBI databases in the same folder, $ ls /data/blastdb/ncbi/nr.* /data/blastdb/ncbi/nr.00.phd /data/blastdb/ncbi/nr.00.phi /data/blastdb/ncbi/nr.00.phr /data/blastdb/ncbi/nr.00.pin /data/blastdb/ncbi/nr.00.pnd /data/blastdb/ncbi/nr.00.pni /data/blastdb/ncbi/nr.00.pog /data/blastdb/ncbi/nr.00.ppd /data/blastdb/ncbi/nr.00.ppi /data/blastdb/ncbi/nr.00.psd /data/blastdb/ncbi/nr.00.psi /data/blastdb/ncbi/nr.00.psq /data/blastdb/ncbi/nr.00.tar.gz /data/blastdb/ncbi/nr.00.tar.gz.md5 ... /data/blastdb/ncbi/nr.10.phd /data/blastdb/ncbi/nr.10.phi /data/blastdb/ncbi/nr.10.phr /data/blastdb/ncbi/nr.10.pin /data/blastdb/ncbi/nr.10.pnd /data/blastdb/ncbi/nr.10.pni /data/blastdb/ncbi/nr.10.pog /data/blastdb/ncbi/nr.10.ppd /data/blastdb/ncbi/nr.10.ppi /data/blastdb/ncbi/nr.10.psd /data/blastdb/ncbi/nr.10.psi /data/blastdb/ncbi/nr.10.psq /data/blastdb/ncbi/nr.10.tar.gz /data/blastdb/ncbi/nr.10.tar.gz.md5 /data/blastdb/ncbi/nr.pal We can then refer to the NR database at the command line as /data/blastdb/ncbi/nr or as just nr if the BLAST database path is configured to check this folder. In this folder we also have other NCBI database, like NT: $ ls /data/blastdb/ncbi/nt.* /data/blastdb/ncbi/nt.00.nhd /data/blastdb/ncbi/nt.00.nhi /data/blastdb/ncbi/nt.00.nhr /data/blastdb/ncbi/nt.00.nin /data/blastdb/ncbi/nt.00.nnd /data/blastdb/ncbi/nt.00.nni /data/blastdb/ncbi/nt.00.nog /data/blastdb/ncbi/nt.00.nsd /data/blastdb/ncbi/nt.00.nsi /data/blastdb/ncbi/nt.00.nsq /data/blastdb/ncbi/nt.00.tar.gz /data/blastdb/ncbi/nt.00.tar.gz.md5 ... /data/blastdb/ncbi/nt.13.nhd /data/blastdb/ncbi/nt.13.nhi /data/blastdb/ncbi/nt.13.nhr /data/blastdb/ncbi/nt.13.nin /data/blastdb/ncbi/nt.13.nnd /data/blastdb/ncbi/nt.13.nni /data/blastdb/ncbi/nt.13.nog /data/blastdb/ncbi/nt.13.nsd /data/blastdb/ncbi/nt.13.nsi /data/blastdb/ncbi/nt.13.nsq /data/blastdb/ncbi/nt.13.tar.gz /data/blastdb/ncbi/nt.13.tar.gz.md5 /data/blastdb/ncbi/nt.nal Note you don't need to keep the *.tar.gz and the *.md5 files once you've verified the checksum (using md5sum to detect any data corruption during download) and decompressed the tar-ball. Peter P.S. This galaxy-users list is meant for discussion of using the tools within Galaxy from an end user perspective. Although there is talk about creating a new Galaxy mailing list specifically for deployment questions like this, currently galaxy-devel is preferred for this kind of discussion.

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galaxy-user April 2013