Ward D comments

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                                            Ward D

Krona chart using diamond blast

Hi, We use krona for the exact same purpose. You can convert the DAA to regular blast output using the diamond view option. This converted output can be used directly...

super long run time for 2 genomes

Hi, Sorry for hijacking the thread, but I am currently encountering something similar. From what I have seen this problem is caused by the mmseqs2 database not being generated properly....

plotHeatmap set multiple yMax values error

Thanks for reporting this, a fix for this sits in #1282, though needs some extra tests. You can stick to an older version, or try to test if the fix...

correctGCbias error

Closing due to inactivity.

the conflict about the pheatmap and multibigwigsummary results

Are you sure you haven't flipped any labels somewhere ? The order in your multibigwigsummary is reversed from what your original command implies, and it seems to be post processed...

plotFingerprint bigwig support

Hi, Thanks for the report. Plotfingerprint indeed doesn't support bigwigs, I've taken the ambiguity out of the docs. That said, support for this could be added, but this will take...

About calculating RPM (reads per million) using bamCoverage.

Hiya, `--normalizeUsing CPM` should do what you need. Kind regards, WardDeb

reformat print line to get rid off unwanted spaces

Thanks @nservant ! and no worries for the delay. I think the conflict came from this line being updated in the devel branch (I forked from master initially). I've resolved...

bamCoverage [multiBamCoverage]

If you need bws / bedgraphs you can run bamCoverage separately for all bam files. The functionality for multiBamCoverage can be found in multiBamSummary.

alignmentSieve returns a truncated bam

Hi, I was able to reproduce, though I'm a bit puzzled about the actual cause. The default chunksize for alignmentSieve has been increased, and this seemed to have fixed the...