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AfshinLab / BLR

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Add genome coverage analysis to pipe #29

Closed pontushojer closed 4 years ago

pontushojer commented 4 years ago

This PR introduces the tool mosdepth to the pipe. This is very useful to calculate coverage statistics and is also implemented as a MultiQC module that create plots (see examples below). This will be verty useful in the report (see https://github.com/FrickTobias/BLR/issues/217).

The conda environment files have also been updated. Note that I have limited the allowed version of both snakemake and bowtie2 as the latest version cause errors in the pipe. These errors are referenced in the comments next to the tools.

Examples of MultiQC plots

mosdepth-coverage-dist-id

mosdepth-coverage-plot-id

mosdepth-coverage-per-contig

This should not be merged before #26 and #27 are merged. Possibly I will have to rebase too.

FrickTobias commented 4 years ago

Looks nice. I think I'd prefer it to be in bar plots, they are quite standard for coverage from what I have seen but the data is definitely good to have!

pontushojer commented 4 years ago

Looks nice. I think I'd prefer it to be in bar plots, they are quite standard for coverage from what I have seen but the data is definitely good to have!

Since the tool generates data files we could quite easily generate our own plots from these later on.

The benefit of these plots are that you can compare across multiple samples should you want to.

FrickTobias commented 4 years ago

Looks nice. I think I'd prefer it to be in bar plots, they are quite standard for coverage from what I have seen but the data is definitely good to have!

Since the tool generates data files we could quite easily generate our own plots from these later on.

The benefit of these plots are that you can compare across multiple samples should you want to.

True and True. Awesome!

pontushojer commented 4 years ago

Will merge this as soon as #23 is merged.