Re: [Useq-users] alternate genomes

[David N. <dav...@gm...>]

Yes, you just need to create a UCSC refflat formatted transcript and gene
table (tab delimited: geneName, transcriptName, chrom, strand,
transcriptStart, transcriptEnd, codingSeqStart, codingSeqEnd, exonCount,
exonStarts(comma delimited), exonEnds), interbase coordinates.  The gene
table is made by merging the transcript table using the MergeUCSCGeneTable
app. See http://useq.sourceforge.net/usageRNASeq.html

-cheers, D

On 10/25/11 8:29 PM, "Youngman, Elaine" <Ela...@um...>
wrote:

>Hello all,
>
>Is it possible to use USeq for genomes other than those in UCSC? I'm
>trying to use it with C. elegans data, and the UCSC version of the genome
>is much older than the version I am using for all of my other analysis.
>
>Thanks!
>Elaine
>
>
>
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