the ways to count number of tags from bam file

[owwa]

Hi guys,

Could you please provide some ways to count the number of tags in bam file?

The view of the bam file (partial) is showed as the following pic:


I need the tag count result as the following format:


Thanks in advance.

[owwa]

It seems that "samtools mpileup" can do similar counting, but it seems that tags will be counted more than once.

[owwa]

need the per base or per 2 base read counts. any idea? thanks.

[GenoMax]

http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html

or samtools depth option.

[rnaeye]

You can take your bam file convert it to samformat using bamtools then sort it by position, then use Unix uniq command with -c option on position column.

[owwa]

http://bedtools.readthedocs.org/en/l...genomecov.html

or samtools depth option.

Thank you! you don't get what i need.

[owwa]

You can take your bam file convert it to samformat using bamtools then sort it by position, then use Unix uniq command with -c option on position column.

Thanks! that's a way. but how to get the per 2 base read counts? in addition, how to filter out some reads which have low mapping quality by this way?