I am trying to use STAR+Cufflinks to do a reference based transcript assembly using unstranded RNA-seq data.
As mentioned in the STAR manual "If you have un-stranded RNA-seq data, and wish to run Cufflinks/Cuffdiff on STAR alignments, you will
need to run STAR with --outSAMstrandField intronMotif option, which will generate the XS strand attribute for all alignments that contain splice junctions"
Thus in the generated SAM file, strand will be derived from the intron motif. Unstranded RNA-seq data will be assigned a strand, which results in a lot of genes have both sense and antisense transcripts in the merged transcript assembly.
My questions are:
1) how reliable is the derived strand info from intron motif?
2) Is the assembled transcripts affected by this?
Thank you very much!
Runxuan
As mentioned in the STAR manual "If you have un-stranded RNA-seq data, and wish to run Cufflinks/Cuffdiff on STAR alignments, you will
need to run STAR with --outSAMstrandField intronMotif option, which will generate the XS strand attribute for all alignments that contain splice junctions"
Thus in the generated SAM file, strand will be derived from the intron motif. Unstranded RNA-seq data will be assigned a strand, which results in a lot of genes have both sense and antisense transcripts in the merged transcript assembly.
My questions are:
1) how reliable is the derived strand info from intron motif?
2) Is the assembled transcripts affected by this?
Thank you very much!
Runxuan
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