Comments (6)
Hello, I think I found the cause of the negative numbers. Int overflow. I noticed that the maximum values of hashtags were suspiciously close to 32768, (as you can see on the table below) which is the maximum value supported by numpy int16: https://het.as.utexas.edu/HET/Software/Numpy/reference/generated/numpy.iinfo.html
I did a quick search on the repo scripts, and I think I found the offending lines, 250 and 251 on processing.py
:
CITE-seq-Count/cite_seq_count/processing.py
Lines 249 to 250 in 7e8b5f0
If you change them to use dtype=int32
that should fix the issue
from cite-seq-count.
Hello @Munfred and thanks for the catch!
I think this might also be linked to the other major issue that hangs the umi correction. I'm working on an update that should come out this week that will include the 16->32 fix and probably the umi correction issue fixed.
from cite-seq-count.
Hi, I just wanted to give you an update I forgot to do earlier
The reason why I was running CITE-seq-Count on the cell hashing dataset is because I wanted to compare it's results with a different demultiplexing approach that uses kallisto.
from cite-seq-count.
Hey @Munfred,
thanks for the heads up and the poster.
Happy to see that results are matching nicely :)
Is this the new "sircel" or is it totally different from this project?
from cite-seq-count.
Hi, sorry for the delay.
This is unrelated to sircel, was a result of the new kallisto bus
feature that let's kallisto process single cell datasets from various technologies.
More info about the BUS format can be found here: https://bustools.github.io/
Some example workflows in python for processing single cell datasets are here: https://github.com/BUStools/BUS_notebooks_python
from cite-seq-count.
This is interesting. I might look into it and use it for dropSeqPipe!
Thanks for the heads up :)
Closing this as the bug was fixed
from cite-seq-count.
Related Issues (20)
- Different "UMIs corrected" results between v1.4.3 and v1.4.5 HOT 2
- Code for running multiple lanes
- ValueError: columns cannot be a set HOT 5
- Python error when there are too many cells? Script never finishes HOT 2
- Cell Hashing on Multiome samples HOT 11
- bug in preprocessing.py -> get_read_paths() (version 1.4.3) HOT 1
- method keeps looking for whitelist when not provided. HOT 8
- 100% unmapped
- Discussion question -- is it normal to take so long? HOT 3
- Include path to tag file in run report HOT 1
- barcodes with 0s in all protein tags and unmapped roll HOT 2
- Running Cite-Seq-count with next GEM protocol HOT 2
- Pandas error after correcting UMIs HOT 1
- Allow to split fastq or get list of readID per cell HOT 2
- Unable to locate temp file while merging results
- Does not compile using Python version > 3.9.x please fix.
- Gene and Antibody both have a pair of fastq files, how to run CITE-seq-Count?
- Please, trim all sequences at the same length.
- CITE-seq-Count run gets stuck
- ValueError: columns cannot be a set HOT 3
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