Number of lines in BAM file?

alexdobin / STAR

RNA-seq aligner

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Number of lines in BAM file? #2084

Open yagam-fluent opened 6 months ago

yagam-fluent commented 6 months ago

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

alexdobin commented 6 months ago

Hi Yigal,

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