I am a newbie to the
NGS studies. I have
PE data (fastq files), and after performing mapping with
bowtie2 I got
bam files. Then I extracted mapped reads using
samtools view -b -F 4 file.bam > mapped.bam
So now I am having
bam file of mapped reads. Are there any tools or programs available to extract information which I need?
I need two things in a single text file:
- First Column: a list (a text file) of mapped reads(IDs) and
- Second Column: a list of regions on the reference genome where the reads are mapped.
For example, "this" is the read or read id which is mapped to "this region" on the reference genome.
read id1 , region 1
read id2 , region 2
So how can I achieve the same? Any help is highly appreciated.