Good Morning Saha: Can you clarify the connection between these utilities and the UCSC genome browser ? Is the getsplicefa.py script reading something from UCSC ?
--Hiram saurav saha wrote: > hello everyone, > > I am working on SOLiD platform and want to use SOLiD data for RNAseq > analysis. For that i am trying to utilize bowtie for mapping an ERANGE for > RPKM. For bowtie mapping we need expanded genome. i am trying to utilize > getsplicefa.py of ERANGE to get splice file. but while doing this is am > getting the following error: > > psyco not running > /share/apps/ERANGE/project/genome/commoncode/getsplicefa.py: version 3.2 > 43180 > 369006 > could not get chr3:72692980-72695247 > could not get chr3:72695415-72695619 > could not get chr3:72695669-72704339 > could not get chr3:72704428-72707527 > could not get chr3:72707652-72708182 > could not get chr3:72708239-72708321 > could not get chr3:72708406-72711003 > could not get chr3:72711152-72712888 > could not get chr3:72713005-72713089 > contt... > > Any help is appreciable > > Saha > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
