Get the "Uniquely mapped reads number" from BAM file

[mguaita]

Hi Alex,

Is there a way with samtools or another tool to get the "Uniquely mapped reads number" of the .Log.final.out file from just the BAM file?

I have already tried converting BAM to FASTQ and realign it with STAR to get the Log.final.out files, and also tried $ samtools view $f | awk '/NH:i:1\t/ {print $1} ' | sort | uniq | wc -l .

However the number of reads reported at the reprocessed Log.final.out and the samtools output do not match.
So I am not very confident.

Thank you very much!

[alexdobin]

Hi Maria,

the command should work... Could you please send me its result and the Log.final.out?
Most outputs (except the number of reads) in the Log.final.out are not easy to reconstruct from the BAM file, unfortunately.
If you need the whole Log.final.out, the only option is to remap using the BAM file as the input.