Dear All,
I have aligned Illumina transcriptome data ( paired-end 100bp) onto genes using bowtie2, which consists of ~10,000 genes.
Now I want to know for EACH GENE,
1) how many reads are aligned concordantly
2) how many reads are aligned discordantly
3) how many reads are aligned as single-end reads
Any help is appreciated.
Thank you,
Christopher
I have aligned Illumina transcriptome data ( paired-end 100bp) onto genes using bowtie2, which consists of ~10,000 genes.
Now I want to know for EACH GENE,
1) how many reads are aligned concordantly
2) how many reads are aligned discordantly
3) how many reads are aligned as single-end reads
Any help is appreciated.
Thank you,
Christopher
Comment