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
>
>
>
>--------------------------------------------------------------------------
>----
>The demand for IT networking professionals continues to grow, and the
>demand for specialized networking skills is growing even more rapidly.
>Take a complimentary Learning@Cisco Self-Assessment and learn
>about Cisco certifications, training, and career opportunities.
>http://p.sf.net/sfu/cisco-dev2dev
>_______________________________________________
>Useq-users mailing list
>Use...@li...
>https://lists.sourceforge.net/lists/listinfo/useq-users
|
