--contig-end-exclusion feature request

[jianshu93]

Dear CoverM team,

In some long read mapping tasks, I need to exclude positions at both ends of the contig but for different length, e.g., left is 100 bp but right is 200 bp et.al. I have no control of the reference sequence created in the lab. Is it possible to also add a second option to include a option for different number of base pairs for left and right end.

Best,
Jianshu

[wwood]

Hi @jianshu93 I'm a bit confused about this one. Generally the references are arbitrarily forward or rev comp, so I don't understand the point of this. And fwd or rev related to the ref or the read?

[jianshu93]

Hi Ben, I think I need to describe my problem more specifically (see attached description). The reference is well know and the reads are pacbio revio II long reads (single end), and there is some synthetic DNA on the reference (not necessary in the middle, can be anywhere on the reference), position known. We want to know the coverage of the synthetic insert DNA. we know the mappings will be on one strand (say forward). So the reference is fixed. I cannot map to the insert DNA alone (e.g., ignore other part on the reference) since I need to pass some filtering (read alignment ratio and identity) to the read and most of the reads are much longer than the insert. What would be you suggestion in the case to have the coverage of the insert DNA.

Best,
Jianshu

mapping_contig_edge.pdf

[wwood]

Ah, it seems like might better be a special case of providing a GFF or BED file, and only calculating the coverage just of the region(s) defined there. That's a long-standing feature request that we've not gotten around to implementing yet - see #16 - is that right?

[jianshu93]

Hi Ben,

It seems yes! I almost forget that I also requested that feature long ago but for different purposes. I would suggest a bed file which we can use any start and end position, and any number of such regions. Then coverage for each region of interest on the background contig. I had a workaround for now, that is we manually edit the reference so that the insert is exaclty in the middle of the contig so that --contig-end-exclusion works since it is the same for left and right.

Best,
Jianshu

[jianshu93]

hi Ben,

Is there a way to have the coverage curve for a given contig, that is coverage at each position and then a curve (perhaps in log scale since coverage varies quite a lot). Or just the number, I can plot it myself. We have the tool for blast based but not for BAM based.

Best,
Jianshu