Aligning to RNA-Seq to Transcriptome using STAR

[kminie]

I want to align RNA-Seq data to Transcriptome using STAR aligner , I can see the option of outSJfilterReads which is for SpliceJunction and by default its ON , is there a way I can turn  it off? Or is there any alternative to use this aligner for  mapping with Transcriptome data ?

[Alexander Dobin]

Hi @kminie

Do you want to map directly to the transcript sequences? Or do you want to map to the genome, and then transform the coordinates to the transcriptome space with --quantMode TranscriptomeSAM ?

Note that --outSJfilterReads will only affect the latter case. In the former case you will want to prohibit splicing with --alignIntronMax 1.

Cheers

Alex