Devon Ryan
Devon Ryan
As noted in gitter and https://github.com/bioconda/bioconda-recipes/issues/41025 CI testing on Azure is currently down. That means that no PRs can be tested or merged at the moment. We've contacted Microsoft but...
We have migrated everything to github actions and packages are building again. Please note that (1) artifacts are still not being stored, (2) the bot will have to be reprogrammed...
InDels themselves will be outside of the calls as well as the context, which is taken from the reference sequence.
Add the appropriate "-Ipath/to/headers" into the CFLAGS variable. Alternatively, just install via conda and then you don't have to deal with any of this.
Since you mentioned deepTools, I'll note that `alignmentSieve` will directly produce the shifted BAM files you're after. As an aside, the tn5 shifting done by the ATAC-seq community is a...
The amount to shift is semi-arbitrary, with the values by which each end of a fragment are to be shifted summing to 9 (this value is due to how the...