Edit 7/20/22: we are reopening this issue for the post-v1 timeline. Ideally, we would like to produce collapsed versions of these SAM files at the conclusion of counting since non-collapsed files can be exceptionally large, so repeat analyses of these alignments might become a time barrier for researchers.
Currently Counter is only able to count alignments from collapsed SAM files produced from tiny-collapse outputs. We would like to extend support for SAM files produced outside of the pipeline, including those containing alignments of fastx collapsed reads.
Reads whose QNAME fields do not contain either a tiny-collapse or fastx_collapser sequence count will be assumed to be un-collapsed and will be assigned a default count of 1 for the alignment.
Edit 7/20/22: we are reopening this issue for the post-v1 timeline. Ideally, we would like to produce collapsed versions of these SAM files at the conclusion of counting since non-collapsed files can be exceptionally large, so repeat analyses of these alignments might become a time barrier for researchers.
Currently Counter is only able to count alignments from collapsed SAM files produced from tiny-collapse outputs. We would like to extend support for SAM files produced outside of the pipeline, including those containing alignments of fastx collapsed reads.
Reads whose QNAME fields do not contain either a tiny-collapse or fastx_collapser sequence count will be assumed to be un-collapsed and will be assigned a default count of 1 for the alignment.