Hello, I have a single-end strand-specific RNA-seq data (Illumina protocol), and I would like to split the bam file in two parts by strand. For the alignment I am using TopHat 2.
However I don't understand how to apply that script to my data since my SAM flags are different (filtering with samtools view -b -f 128 -F 16 etc. give me an empty file).
samtools view sample.bam | cut -f2 | sort | uniq
0x0 (0) 0x10 (16 r read reverse strand) 0x100 (256 s not primary alignment) 0x110 (272 rs read reverse strand + not primary alignment)
Can anyone help me?
Thanks very much!