Comments (8)
from cite-seq-count.
Hi,
I set the cells parameter to 1million, just thinking of retrieving empty droplets. That's too high right?
from cite-seq-count.
from cite-seq-count.
hi, I need to retrieve the empty droplets for the sake of normalization, to model noise component. I have run your method about a year ago and you can see I posted a different issue here about totalseqB #158
but the point is I used high number of cells as you can see in my run info to retrieve the empty droplets.
I tried again with inputting the raw unfiltered cellranger barcodes list as a whitelist for my data
and kept the -cells argument at 1million cells , it still keeps getting stuck at the final step for hours! and it looks like it's trying to process more than 1million!
I think something has changed in the new version, because it ran fine on all my previous totalseqA data..
from cite-seq-count.
from cite-seq-count.
thank you so much for your prompt response! I tried reinstalling the older version( 1.4.3) and I seem to have resolved this. However, I tried to reproduce my previous analysis, I seem to have a new issue with both new and old version where it fails at the very last step!
any ideas? :(
from cite-seq-count.
from cite-seq-count.
yes, it is! installed python 3.7 and worked! thank you so much!
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
- 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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