Hi Manuel

you can use the flags in the bam files to extract the reads mapping in sense/antisense. Let's assume that you have single-end reads and you want the reads mapping in the positive strand, you can use this command:

samtools view -F 16 -b -o positive_strand.bam INPUT.BAM

-F means that you want to discard the reads with the flag 16. This flag is for the reads mapping on the negative strand.

If you want the reads mapping on the negative strand:

samtools view -f 16 -b -o positive_strand.bam INPUT.BAM

You can look at this website to see the flags corresponding to different combinations of mapping features: https://broadinstitute.github.io/picard/explain-flags.html

I hope this can be helpful,

Riccardo

Hi Manuel

you can use the flags in the bam files to extract the reads mapping in sense/antisense. Let's assume that you have single-end reads and you want the reads mapping in the positive strand, you can use this command:

samtools view -F 16 -b -o positive_strand.bam INPUT.BAM

-F means that you want to discard the reads with the flag 16. This flag is for the reads mapping on the negative strand.

If you want the reads mapping on the negative strand:

samtools view -f 16 -b -o positive_strand.bam INPUT.BAM

You can look at this website to see the flags corresponding to different combinations of mapping features: https://broadinstitute.github.io/picard/explain-flags.html

I hope this can be helpful,

Riccardo

I can suggest you to follow this:

https://www.biostars.org/p/92935/