I did a tophat/2.0.13
alignment giving both genomic and transcriptome inputs and would like to know how I can find %reads mapped to transcriptome and %ampped to the genome in my accepted_hits.bam
output file.
Is there a straight forward way of doing this? samtools flagstat
only give me overall mapping % and does not distinguish between genomic and transcriptomic alignment.
Below is the script I used to for the tophat alignment:
tophat -G GRCm38_p4.gtf --min-anchor 8 --min-isoform-fraction 0.15
--library-type fr-unstranded --transcriptome-index known_mm10 -p 12
-o ${stdout} /Bowtie2Index/genome /R1.fastq /R2.fastq
Any resources/suggestions would be appreciated.
Thank you,