STAR aligner - multimaps vs. strandedness
0
0
Entering edit mode
6 months ago
cjag • 0

Hi,

I'm trying to use STAR aligner for ribosome profiling libraries, which have are directional due to the library kit I used (NEB small RNA). But the generally accepted workflow for ribosome profiling read alignment involves eliminating reads which map more than once to the genome (i.e. STAR parameters of --outFilterMismatchNmax 2 --quantMode TranscriptomeSAM GeneCounts --outSAMattributes MD NH --outFilterMultimapNmax 1). As far as I understand it, STAR does not distinguish strandedness in any way other than the geneCounts table output. So, does this that I am losing data by discarding reads which multimap when processed as unstranded, but aren't actually multimappers because they should only be aligned in one direction? If so, does anyone know of a way to get around this issue? Should I expand my multimapping allowance and then do a quantification on the BAM output with a tool that can distinguish read direction (but then how do I make sure the quantification tool only counts the best-scoring read for the proper direction?)?

Similarly, I have been pre-filtering reads against rRNA/tRNA/snRNA with Bowtie prior to STAR alignment, but if I'm not specifying strandedness in that step, could I be losing a lot of reads that might actually be legitimate mRNA-mapping reads? If anyone has suggestions for alternative tools that allow for specifying directionality, that would be greatly appreciated.

Thank you!

RNA-Seq alignment ribosome profiling riboseq STAR • 287 views
ADD COMMENT

Login before adding your answer.

Traffic: 2557 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6