[Bioperl-l] adding tags to BAM aligned reads

Bilbo jonas.zierer at googlemail.com
Fri Jun 3 08:51:54 UTC 2011


Hi everybody,

I have a bam file and use bioperl (Bio::DB::Sam) to work with it.
Now i wanted to ask if there is any possibility to add tags to aligned
reads in this File?

i use

my $iterator     = $bam->features(-iterator => 1, -flags    =>
{M_UNMAPPED=>0});
while (my $align = $iterator->next_seq) {
        ...
}

to loop through the aligned reads and I am searching for anthing like

$align->addTag(key=>value)


and i have one more question: is it possible to get the coverage of a
segment using only the read start positions?

Thx
bye



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