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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The lab I work with would like to compare a few populations' genomes of a species with an unpublished genome assembly.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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Gain sequences after mapping reads to a reference genome
by zwp112358 29 Apr '13

29 Apr '13

Hi all, I would like to know if mapping reads to a reference genome, through galaxy, can generate the query genome sequence? I had mapped my reads from Illumina sequencer to a reference genome through both BWA and Bowtie on Galaxy public server platform(https://main.g2.bx.psu.edu/root ). As a result, i gained the SAM files. But, i can't find how to generate the resulted assemblied genome sequence. Is there anyone know this? Any reply will be very appreciated. Best regards. Weiping Weiping Zhang, Doctor candidate; School of bioengineering, Jiangnan University; Lihu Roads 1800#, WUXI, Jiangsu; Zip Code: 214122

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gff installation failed with easy_install
by Mic 29 Apr '13

29 Apr '13

Hi, I have tried to install gff with easy_install, but I got the following error: $ easy_install --prefix=/home/mic/apps/pymodules -UZ https://github.com/chapmanb/bcbb/tree/master/gff Downloading https://github.com/chapmanb/bcbb/tree/master/gff error: Unexpected HTML page found at https://github.com/chapmanb/bcbb/tree/master/gff How is it possible to install gff? Thank you in advance. Mic

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GenBank database files
by Mike Dyall-Smith 28 Apr '13

28 Apr '13

This should be easy (but not for me so far). I want to do local blast searches, so I download the premade nr protein blast database from GenBank. It is split into 10 .tar.gz files. I've decompressed them all, and now I want to put all the file parts together. Can I simply concatenate all similar files? (e.g. all 10 parts of the .phd files). The Readme mentions use of an alias file, but I did not find this at all clear. A set of step-by-step decompression and restoration instructions would be useful. I could not find any. Thanks for any assistance, Mike DS Sent from my iPhone4

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Regarding combining several txt files and producing one fastq file
by Jennifer Jackson 28 Apr '13

28 Apr '13

Hi Yona, To merge together multiple datasets this way, use the tool "Text Manipulation -> Concatenate datasets tail-to-head". This works on two datasets at a time, so you may need to run it a few times if you have more than that, adding in a new file to the master merged file with each run. Watch out for introducing blank lines (unintentionally) between the files. To remove them should any be present (it doesn't harm a file if none are there), after you have merged all the files together, use the tool "Filter and Sort -> Select" with: option: NOT Matching and the expression: ^$ Once you are sure that the merged file is correct, you can permanently delete the working files to recover disk space. "FastQC" and/or "FASTQ Groomer" are generally both good at detecting format problems. http://wiki.galaxyproject.org/Support#Error_from_tools Good luck with your project, Jen Galaxy team On 4/27/13 8:23 PM, Yona Kim wrote: > Dear Jennifer > > I was wondering if there is a tool in galaxy that combines several txt > files (which I got from decompressing fastq.tgz file) and produce one > fastq file from them. > > I was searching it in google and read your previous email to somebody > else and you mentioned about the tool "cat" which seems to be the > right tool for me to use to combine these txt files in order to > produce one fastq file.. but I can't find this tool.. > > any advice? > > Thank you very much and I always appreciate your help very much!! > > Bests, > > Yona Kim > > -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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problem with the public Main Galaxy server
by Ianiri, Giuseppe 27 Apr '13

27 Apr '13

Hi, is anybody else experiencing problems with the public Main Galaxy server at http://main.g2.bx.psu.edu? It just does not work anymore. Any suggestion? Giuseppe Ianiri

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Barcode splitter on paired end Illumina reads
by Veranja Liyanapathirana 27 Apr '13

27 Apr '13

Dear Galaxy team I am so sorry for repeatedly posting the same question, but I do need some inputs in to this. Please let mek now the best way to use barcode splitter on Paired end Miseq data. The data is already split for the Illumina indexes using Miseq reporter, what I want to do is to split some inhouse barcodes within each of the sample. Barcodes are there in both 5' and 3' end but they are both the same. Please let me know if the best practise is to 1. Join read 1 and two - barcode split and split the two reads 2. Split Read 1 and 2 and them join using FastQ joiner and split again Basically I want to exclude any reads where the same numbered reads are not categorised in to the same barcode. Thanks Kind Regards, Veranja Veranja Liyanapathirana Graduate student Microbiology, CUHK

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