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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,

Yuka Takemon
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  • Note that there is now a beta bioinformatics stackexchange site where this question might receive answers: https://bioinformatics.stackexchange.com/ – bli May 24 '17 at 12:39

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