Hello,
This question should be of general interest, and judging from documentation/publication I am not sure about the issue, so here it goes:
In Bismark, where can I see the number of non-BS-mismatches in aligned reads (i.e. in the SAM file)?
I'm especially asking whether the number ## in NM:i:## is reliable. As I understand, it reflects only the true non-BS-mismatches (no C->T and no G->A conversion), since it is always lower than the number of total methylated+unmethylated positions.
So, I'd just like to be sure that BS-mismatches aren't in any way taken into account in the number of the NM string.
I'm interested in Bismark's behavior but note that this question may also be interesting for other mappers like bsmap, which might report differently here.
Thanks!
This question should be of general interest, and judging from documentation/publication I am not sure about the issue, so here it goes:
In Bismark, where can I see the number of non-BS-mismatches in aligned reads (i.e. in the SAM file)?
I'm especially asking whether the number ## in NM:i:## is reliable. As I understand, it reflects only the true non-BS-mismatches (no C->T and no G->A conversion), since it is always lower than the number of total methylated+unmethylated positions.
So, I'd just like to be sure that BS-mismatches aren't in any way taken into account in the number of the NM string.
I'm interested in Bismark's behavior but note that this question may also be interesting for other mappers like bsmap, which might report differently here.
Thanks!
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