deeptools
plotFingerprint bigwig support
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!
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.
