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

CpG Masking changing alignment length?
by Michael E. Steiper 19 Mar '11

19 Mar '11

Hi All, I have a general question about CpG masking. I have a .maf file, when I use the maf to fasta tool, it gives me an alignment of 2,735,329 bp. But if I CpG mask the .maf file (restricted definition) then I use the maf to fasta tool, I get a very different alignment length, 5,572,544 bp. It would be great to know what is the cause of these differences. THANKS! Mike

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Indel Output - what is this mystery column?
by John David Osborne 19 Mar '11

19 Mar '11

Hi, I was running an indel analysis on galaxy and I got a file as output that has rows that look like this: fly2 9829 9830 I ATACTCCAA 79 Can anybody tell me what the last column (79) means? There is obviously an insertion at 9829 with those nucleotides, but I'm not sure what the 79 refers to even after reading the linked documentation. Is it the number of reads that had this? A quality score? -John

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showing content of 2 columns in select
by andrew stewart 18 Mar '11

18 Mar '11

Hi, I would like to be able to show the content of 2 columns from a file as the name of options in a select. Example : I have a file with: Column_1 Column_2 Column_3 I have a select field which feeds its values from this file The value for each choice is Column_1, but I would like the name (i.e. what the user sees) to be a combination of Column_2 and Column_3 (in this case, Column_3 contains a count, which would be shown between parenthesis) Is there a way to do that without resorting to the deprecated <code> tag ? (with actions maybe ?) Thanks

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extracting raw count data from mapping
by Austin Paul 18 Mar '11

18 Mar '11

Hi, I would like to extract raw counts from tophat output. Does anyone know a way to do this in Galaxy? Thanks!

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Fwd: [galaxy-bugs] to view raw data in ucsc browser
by Anton Nekrutenko 17 Mar '11

17 Mar '11

Begin forwarded message: > From: Anne LE MOUEL <alemouel13(a)gmail.com> > Date: March 16, 2011 10:57:42 AM EDT > To: galaxy-bugs(a)bx.psu.edu > Subject: [galaxy-bugs] to view raw data in ucsc browser > > > When I wanted to view the reads in ucsc browser 2 month ago (1st upload on the power point) , it was possible and now (2nd upload on the powerpoint) it is not proposed : ? > I'd like to view the reads in order to compare them with the MACS peaks. > Thank you for your answer, > Best regards > Anne Le Mouël > > -- > ***************************************************** > UMR7216 Epigénétique et Destin Cellulaire > Interface entre Développement et Environnement (Valérie Mezger) > Université Paris Diderot, 35 rue Hélène Brion, case 7042 > 75205 Paris Cedex 13 > Tel: +33 (0)1 57 27 89 25 > Fax: +33 (0)1 57 27 89 11 > ************************************************* > On ne fait jamais assez provision de ceux qu'on aime (Anatole Le Braz) > > > > -- > ***************************************************** > UMR7216 Epigénétique et Destin Cellulaire > Interface entre Développement et Environnement (Valérie Mezger) > Université Paris Diderot, 35 rue Hélène Brion, case 7042 > 75205 Paris Cedex 13 > Tel: +33 (0)1 57 27 89 25 > Fax: +33 (0)1 57 27 89 11 > ************************************************* > On ne fait jamais assez provision de ceux qu'on aime (Anatole Le Braz) > _______________________________________________ > galaxy-bugs mailing list > galaxy-bugs(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-bugs

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Re: [galaxy-user] [galaxy-bugs] raw data reads in Galaxy
by Anton Nekrutenko 17 Mar '11

17 Mar '11

Anne: 1. This question is more appropriate for galaxy-user list, so I'm forwarding this e-mail. 2. When you map reads against a reference these initial dataset is your raw reads (or perhaps I do not fully understand your question). Thanks! anton galaxy team On Mar 16, 2011, at 10:58 AM, Anne LE MOUEL wrote: > How to see the raw data of the reads mapped on galaxy, > Thank you > Best regards > Anne Le Mouël > > -- > ***************************************************** > UMR7216 Epigénétique et Destin Cellulaire > Interface entre Développement et Environnement (Valérie Mezger) > Université Paris Diderot, 35 rue Hélène Brion, case 7042 > 75205 Paris Cedex 13 > Tel: +33 (0)1 57 27 89 25 > Fax: +33 (0)1 57 27 89 11 > ************************************************* > On ne fait jamais assez provision de ceux qu'on aime (Anatole Le Braz) > _______________________________________________ > galaxy-bugs mailing list > galaxy-bugs(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-bugs

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Galaxy on Cloud not recognizing .txt files as fastq
by karlerhard＠berkeley.edu 17 Mar '11

17 Mar '11

Hello, I have been able to get Galaxy to instantiate on our Cloud account, and would like to use the NGS tools to trim and map Illumina libraries. However, when I tried to import .txt files (the data contained in these files are in fastq format) located in an S3 bucket, Galaxy did not recognize them as fastq data. I tried to import the files via the URL of the S3 bucket, and Galaxy just imported the actual name of the URL rather than the file itself. Do I need to change the extension of these .txt files to .fastq? Or have I gotten something wrong with respect to the location of the data in the S3 bucket? thanks for any help! karl

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Postdoc position
by Abderrahman Khila, Dr 16 Mar '11

16 Mar '11

Dear Galaxy users, I am hoping if you could please take note and distribute the attached Postdoc ad among people who might be interested. My lab is looking for someone who can lead a genome/transcriptome assembly and annotation project. The candidate will also have the possibility of combining their Bioinfo skill with the lab’s expertise in studying gene function and evolution. Thank you in advance for your help. Best whishes. A Khila ------ Group Leader Institute of functional genomics Lyon, France

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Error on Indel Analysis Tool
by Evan Schwab 16 Mar '11

16 Mar '11

Hi, I am receiving the following error when I try to run the Indel Analysis tool on a sam file. I kept the Frequency threshold at the default 0.015. Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/indels/indel_analysis.py", line 227, in if __name__=="__main__": __main__() File "/galaxy/home/g2main/galaxy_main/tools/indels/indel_analysis.py", line 84, in __main__ add_to_mis_matches( mis_matches[ chrom ], pos, bases ) File "/galaxy/home/g2main/galaxy_main/tools/indels/indel_analysis.py", line 34, in add_to_mis_matches mis_matches[ pos + j ] = { base: 1 } MemoryError Prior to that I tried with Frequency threshold 0.0 and it ran for days on end without any results. And I've tried Frequency threshold of 0.10 and it gave and error that said "Killed" with no explaination. Is there an error with the tool? Thanks Evan -- Evan Schwab Research Associate Megason Lab Department of Systems Biology Harvard Medical School 200 Longwood Ave Boston, MA 02115 908-938-3779

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library features
by Belinda M. Giardine 16 Mar '11

16 Mar '11

I have been working with the libraries and found some features that would make things much easier. Sometimes files get loaded into the wrong folder, it would be nice to be able to move the file to another folder rather than delete and reload it. Also the option of importing data into the library from a history is not available when updating a file. The work around is to load the new and delete the old, but you lose the history of the file changes that way. Thanks, Belinda

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