Number of lines in BAM file?

[yagam-fluent]

Hi Alex,

Is there a way to know the total number of lines in the BAM file from any of the STAR outputs? The log outputs the total number of multimapped reads, but not how many alignments there are.

Thanks,
Yigal

[Alexander Dobin]

Hi Yigal,

STAR does not output such a number, so you would need to count the lines.