plotFingerprint bigwig support

[annajbott]

Hello,

I was wondering if plotFingerprint supports bigwig input files?

The documentation mentions using bigwigs or indexed BAM files as input: https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html (plotFingerprint randomly samples genome regions (bins) of a specified length and sums the per-base coverage in indexed [BAM][] (or bigWig) files that overlap with those regions), but I don't think bigwigs are actually supported. Could this be added as a feature?

Deeptools version = deeptools 3.5.1
Python version = Python 3.8.18

Command:

plotFingerprint -b test.bw -plot test.png --blackListFileName test_blacklist.bed --region chr10:25249964:25252083 --outQualityMetrics test_QC.tsv --outRawCounts test_counts.tab

Screen ouput:
[E::hts_hopen] Failed to open file test.bw

The same command works with indexed bams, so I assume its two typos in the documentation that mention bigwig files (unless I'm missing a flag or something). I can use BAMs, but bigwigs would be much preferred for my usage of plotFingerprint. Thanks!

[WardDeb]

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 a bit more time to implement.