User: vasu punj

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vasu punj360
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Posts by vasu punj

<prev • 36 results • page 1 of 4 • next >
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Answer: A: Cufflinks Transcript-Extract
... You should be able to do in Biomart I think fetch seq shoudl also allow you to do the same. Vasu ________________________________ Subject: Fwd: [galaxy-user] Cufflinks transcript-extract Hi, I use cufflinks to assemble my RNA-Seq reads which produced a GTF file, such as follows:(1)chr1 Cufflinks ...
written 6.2 years ago by vasu punj360
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Comment: C: Bed To Bam Conversion In Galaxy
... Jen,   I ran the flow as you suggested, but got following error message, Do You hav eany suggestion? I added 0 and flips the columns: Here is the few lines of input file: chr1 12137 12336 61R33AAXX100706:1:79:7707:9270 0 - chr1 31542 31741 61R33AAXX100706:1:37:11341:10600 1 - chr1 39921 40120 ...
written 6.3 years ago by vasu punj360
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Answer: A: Annotation File For Cufflinks
... UCSC should work fine.   Vasu Subject: RE: [galaxy-user] annotation file for cufflinks To: "vasu punj" , "Jennifer Jackson" , "galaxy-user" Date: Tuesday, August 30, 2011, 10:53 PM Hi I have down-loaded UCSC HG19 annotation files from Cufflinks; Should I just load genes.GTF file (about 100 MB ...
written 6.4 years ago by vasu punj360
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Answer: A: Annotation File For Cufflinks
... If using Ensembl make sure it is properly formatted. Vasu Subject: [galaxy-user] annotation file for cufflinks To: "Jennifer Jackson" , "galaxy-user" Date: Tuesday, August 30, 2011, 1:52 PM Hi jen and galaxy users, when I try to use cufflinks in GALAXY and select "use reference annotation", I ...
written 6.4 years ago by vasu punj360
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Comment: C: Mi-Tools- Tools_Fabfile.Py Permissions Requirements (Local Install)
... IGV should allow you to do this  but not sure about trackbrowser in Galaxy. Vasu Subject: [galaxy-user] visualization To: "galaxy-user@lists.bx.psu.edu" Date: Wednesday, August 3, 2011, 6:03 PM Hi Jen, I mapped illumine reads to draft genomic contigs, and try to visualize the mapping. Is ther ...
written 6.5 years ago by vasu punj360
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Comment: C: Calculating Percent Coverage Over The Target Genome
... Jen/ Jeremy/ Galaxy team,   Is there any plan of implementing gene fusion version of TopHat in Galaxy perhaps in next few months or so? Alternatively, if some one has used with gene fusion using TopHat in Galaxy frame work please share.   Thanks.   Vasu Punj ...
written 6.5 years ago by vasu punj360
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Answer: A: Query
... It appear that you are talking about RNA-seq data analysis. If so please read a tutorial posted by Jeremy to get an idea how the work flow has to be used. I am sure folks would also like to know what error you are getting. Subject: [galaxy-user] query To: galaxy-user@lists.bx.psu.edu Date: Thursd ...
written 6.5 years ago by vasu punj360
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Comment: C: Cufflinks Reporting Fpkm Values Of All Zeroes (0)
... It appear that you are now using Ensembl  make suer it is properly formated- Chr is added to first column. It may be worth checking.   Vasu Subject: Re: [galaxy-user] Cufflinks reporting FPKM values of all zeroes (0) To: "David K Crossman" Cc: "galaxy-user (galaxy-user@lists.bx.psu.edu)" Date: ...
written 6.5 years ago by vasu punj360
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Answer: A: Rna-Seq Cds, Splicing And Tss Fails
... your pid must also be empty. I think: -s Causes cuffcompare to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case b ...
written 6.5 years ago by vasu punj360
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Comment: C: Re: Looking For New Transcripts With Cufflinks
... Will submit to Galaxy my additions. Thanks Vasu Subject: Re: [galaxy-user] Looking for new transcripts with cufflinks To: "vasu punj" Cc: "GavinOliver" , "David Matthews" , "galaxy-user" Date: Wednesday, July 6, 2011, 10:08 AM One question related to this If I am intrested in annota ...
written 6.5 years ago by vasu punj360

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