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Old 07-12-2011, 06:16 AM   #1
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Join Date: Jun 2010
Posts: 15
Default how to generate corresponding gene annotation for a combined assembly

Hi All,

I am trying to get a fully combined gene annotation for a combined assembly of Bos taurus, ovid Arosa and de Novo Ovis Aries for the mapping. This is a published sheep data on 2011. btw, In this paper, they only provide a combined assembly fasta genome sequence file and SRR files sequence file for each sample.

so i ran some RNAseq tools, bowtie, tophat, and cufflinks with provided files from the paper. as you know but from the ouput of cufflinks, there is only cuffid1, cuffid2....i need a standard gene symbols such as uscs gene annotation or emsembl or refseq id to interpret the results and to do further analyses.

so. it seems cuffcompare can do it with gtf file. here, i have a newbie question. how can i generate exactly a corresponding combined gene annotation gtf file of Bos taurus, ovid Arosa, and de Novo Ovis Aries for the combined assembly fasta .fa file? I need exactly matched annotation file with the fasta file, anyone who can advise me in details?

it would be very appreciated- Thank you so much, CH.
hibachings2013 is offline   Reply With Quote

bowtie, cuffcompare, cufflinks, gene annotation, tophat

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