Open kerenzhou062 opened 2 years ago
Generally speaking, the algorithm counts each read with the strand it is reported in the BAM file. There's no general reason to do otherwise, as some pair-ends might behave differently.
An approach I would advice could be to focus on either the first or the second pair, for example with the -F
flag you can exclude the second pair from the analysis.
In bamtocounts 2.7 (https://telatin.github.io/bamtocov/tools/bamtocounts.html), for example, I added the --paired
mode that counts fragments rather than reads (thus focusing on the first read strand), but in BamToCov this would not be the general use.
As for the second question, --extendReads
is being updated (but still experimental) and I will be back to you with the next release :)
@telatin Dear Dr. Telatin,
I'm curious about how
bamtocov
deal with paired-end bam from stranded libraries by setting with--stranded
.Will
bamtocov
automatically treat mated reads as reverse strand? For example, ifmate1
of a fragment was recorded as '-' strand in bam, which means thatmate1
are actually comes from '+' strand. When setting with--stranded
,mate1
will be counted as '+' strand. My question is, willmate2
of this fragment be automatically counted as '+' strand as well in this case?Also, will the new '--extendReads INT' parameter also work well with paired-end bam?
Best,
Keren