Rna-Seq Read Mapping Stats/Metrics

Question

[pm2013]

Hi

I am trying to get some stats regarding my RNA-seq alignment to see how many reads are mapped to exon, intron, junctions and intergenic regions. Our group used sammate alignment report in the past that gave % reads mapping to each of the four regions. However, we have been having trouble with it recently as it gives diff results for the same .bam files when different versions are used or doesn't give % for some regions (intergenic & junctions). I tried RNAseqQC and picard tool's CollectRnaSeqMetrics but they seem to give info in terms of bases. Also I can't seem to get metrics for junctions. Are there any other tools for this? Any help would be really appreciated.

Thanks

Answer 1

[Mikael Huss]

I like RSeQC for this purpose (although the name is unwieldy and similar to RNAseQC). It does what you want (check how many reads are mapped to exon, intron, junctions and intergenic regions) and many other things in addition.

[pm2013]

Thanks. I had looked into it but how do I get junction reads? My impression is it only annotates the junction reads into known, novel partial novel?

[Mikael Huss]

I guess you are right, I had somehow assumed that it returned stats on junction reads too. It's strange that it doesn't, as it's so thorough in other ways. When I want to quantify junction reads, I usually use some simple grep command that reports the number of CIGAR strings with an N in them.