isolate the output of lignment in fastq format

Question

[alireza346]

I have RNAseq data and trying to align the fastq files to human transcriptome (not genome). I want to isolate the reads that map to mRNA transcriptome in fastq format. I am using bowtie2. do you know how I can get the output of bowtie2 as fastq file?

Answer 1

[corend]

Converting Bam To Fastq