I got few SOLID RNA-Seq files which I am trying to map to some "draft+ quality" mammalian genome. So far I tried:
bowtie 0.12.7 (unspliced mode)
tophat 1.3.1 (spliced)
ab_wtp_1.2.1 (spliced)
Bowtie works OK but obviously misses spliced reads. Tophat without annotations maps less reads than bowtie. Whole Transcriptome Pipeline gives me colorspace gff file which then GffToSam fails to convert to SAM (error: "doesn't have F3 or R3 tag. Skipping.").
I wonder what is being currently used to map SOLID RNA-Seq data in spliced mode and get viewable in IGV SAM/BAM files in the end?
Any information about ab_wtp (or other software) config.ini files will be very helpful.
bowtie 0.12.7 (unspliced mode)
tophat 1.3.1 (spliced)
ab_wtp_1.2.1 (spliced)
Bowtie works OK but obviously misses spliced reads. Tophat without annotations maps less reads than bowtie. Whole Transcriptome Pipeline gives me colorspace gff file which then GffToSam fails to convert to SAM (error: "doesn't have F3 or R3 tag. Skipping.").
I wonder what is being currently used to map SOLID RNA-Seq data in spliced mode and get viewable in IGV SAM/BAM files in the end?
Any information about ab_wtp (or other software) config.ini files will be very helpful.