All reads from the bam file

Question

[Eva_Maria]

Hi, Is there any way to get mapped and unmapped reads from a bam file (from Star aligner )? I need to look for gene coordinates.

Answer 1

[GenoMax]

You can simply process BAM file with samtools to separate the reads: How To Filter Mapped Reads With Samtools and combine this with samtools fastq to get fastq formatted reads.

or

use following option for STAR.

outReadsUnmapped                None
                                Fastx   ... output in separate fasta/fastq files, Unmapped.out.mate1/2