Closed vivekbhr closed 8 years ago
The current implementation is summarized here: https://github.com/fidelram/deepTools/blob/feature/riboseq_352/deeptools/bamCoverage.py#L227-L264
Do you need PE reads? That's an easy enough extension. Can you think of a context where specifying the strand wouldn't be useful? I suppose the DNase-seq cases that Anäis presented yesterday would be examples of that.
Most CAGE data out there is single-end, though there are other protocols that rely on paired-end seq. So it would be good to have it for both.
Strand will sure be needed for CAGE but maybe not for DNAse/MNAse etc..
I'll work on this a bit tomorrow in the riboseq branch, where it's mostly implemented already, and then merge it into develop.
OK, this is fully implemented now. SE and PE reads are supported, positive and negative offsets are also supported. As an example, from here on out, --Offset 1
will use only the first base of each alignment (after accounting for orientation. Note that the --MNase
option is different, since it centers on the 2 or 3 bases at the middle of fragments, whereas --Offset
is used on the read level.
I'll update the Galaxy wrappers and then merge that branch (thereafter closing this issue).
I've just merged this into develop
.
For generating CAGE coverage files from bamcovergae. It will be good to allow generating 1 bp binned bam files where only 5' -most base-pairs are kept (keeping in mind the RNA-strand).
This is already implemented somewhere in Ribo-Seq branch, as @dpryan79 said.. So we will clean it up when merged..