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Bam tag histogram mrfifo #103
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…er. Missing functionality - paired end RNA-seq (non-barcoded) - single end RNA-seq w custom barcode - multiple input files with per-input parameters
…ls like header to output to make it 100% compatible
…rules in main.smk accordingly. Needs real world testing
…occur downstream though...
Thanks so much for the amazing code, Marvin! I started testing on the tiny spatial data and Open-ST mouse hippocampus, and ran into some minor issues:
As soon as the tests finish on the Open-ST data, I will report back and we can merge this into fast-cmdline and master. Also, I will run on very large Open-ST data (>10B reads) to explore the limits of the pipeline in terms of mem usage. |
It worked with the tiny data, but then the Edit: the default |
Tested, works as advertised :) Maybe @nukappa can run another sample, but LGTM as soon as we address the minor points above (making sure installation works fine, and the |
@marvin-jens will address in
This was fixed
This is not necessary yet
Ready to test by @nukappa and merge into |
Replacing dropseq-tools BamTagHistogram
This tool has become a pain-point as we now routinely have hundreds of millions of legitimate, spatial barcodes in open-st data.
This PR features a complete, drop-in replacement re-written in python using
mrfifo
. It is about 10x faster and uses less RAM. I've included unit test code and also run it on some real-world data, observing identical output compared to dropseq-tools.Unless you run into issues, I'd like to merge this into fast-cmdline (and possibly master) asap.
Best,
-Marvin