megadepth
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ChristopherWilks
BigWig and BAM utilities
--Hi, is there an equivalent command to this one with megadepth: from bedtools i can output coverage per base with: genomeCoverageBed -d -i chr20.bed -g chr20_size.genome thank you --
Hi, megadepth has been a great tool! Thanks for the excellent utility! One question: is there an option to include a scaling factor when converting BAM to BigWig? Both UCSC...
From the code, `process_jx_output.sh` always outputs only `0` in the strand column. I imagine it's because the `megadepth --all-junctions` column 5 only gives the mapping strand, which would be incorrect...
alts output is 0-based, yet junction output is 1-based. Might make sense to pick one of these for all output files.
When I use megadepth with `--alts`, the file output has a TSV extension though it's comma-separated. Can address the issue the obvious way, but I'm very happy to help change...
Hello, Thanks a lot for creating megadepth! Its bam processing capabilities seem great and extremely fast. I was wondering whether some bigwig functionalities could still be implemented. Specifically, I was...
In many applications, it's useful to grep for variants by locus. It'd be very convenient if megadepth output wrote contig names instead of their corresponding numerical ids from the BAM,...
Hi, Thank you for creating this wonderful tool. I am using it in one of my nextflow workflows and I have noticed some unexpected behaviours which are as follows: Image...
relevant issue: https://github.com/LieberInstitute/megadepth/issues/6 I am trying to build megadepth on alpine container in order to have a "slimmer" image in the end. I get various issues from compiling. the image...
