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A question about the direction of 6th 5mC if C+m?5,2 is shown in a reverse strand read
After basecalling and alignment ,the bam gives us modification information. If there is a reverse strand read, the sequence "ACCGGT..." is alligned to the forward strand?And I don't know the direction of 6th 5mC if C+m?5,2 is shown in a reverse strand read ,is it from the begining of 5'end of this reverse read?
Hi @wtfeng111,
The modbase tag specification annotations state the strandedness of the modifications. This information allows for modifications on 2d reads to be annotated by indicating on which strand the modification was observed. The table below shows how forward and reverse complement reads with top (+) and bottom (-) modifications are resolved in reference space.
For example, a reverse complement aligned read (-) with modifications on the bottom-strand (-) will be resolved to the forward strand (+) aligned in the reference direction.
| Strandedness in output file | SEQ direction according to FLAG | ||
|---|---|---|---|
| 0x10 not set (i.e. forward alignment) | 0x10 set (i.e. reverse-complement alignment) | ||
| Modification Tag Strandedness |
+ |
+ |
- |
|
- |
- |
+ |
|
In your example, you have a forward alignment (+) and the mod is on the top (+) so your modification indexing is in the forward reference direction.
The ModKit tools might also have something useful to view the mods as an annotated bed file.
Kind regards, Rich
