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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, if mate1 of a fragment was recorded as '-' strand in bam, which means that mate1 are actually comes from '+' strand. When setting with --stranded, mate1 will be counted as '+' strand. My question is, will mate2 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
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How bamtocov deal with paired-end bam from stranded libraries?
How did bamtocov deal with paired-end bam from stranded libraries?
Apr 4, 2022
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
The text was updated successfully, but these errors were encountered: