Comments (8)
Hoohm
commented on July 26, 2024
Hello,
How many cells are you looking for? Might be that the parameter is set too
high
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On Thu, Feb 23, 2023, 15:47 naila53 ***@***.***> wrote:
Hi,
I'm trying to run Cite-seq-count without a whitelist argument, however, it
keeps being stuck at the looking for whitelist step after finishing the
mapping for hours!
[image: image]
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naila53
commented on July 26, 2024
Hi,
I set the cells parameter to 1million, just thinking of retrieving empty droplets. That's too high right?
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Hoohm
commented on July 26, 2024
You should set it to the expected cells.
I think I add 20% to be sure to capture all possible cells.
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On Fri, Feb 24, 2023, 16:13 naila53 ***@***.***> wrote:
Hi,
I set the cells parameter to 1million, just thinking of retrieving empty
droplets. That's too high right?
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naila53
commented on July 26, 2024
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..
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Hoohm
commented on July 26, 2024
Interesting.
I can't get into it atm as I'm on holiday.
I suggest you try the older version then.
https://stackoverflow.com/questions/5226311/installing-specific-package-version-with-pip#5226504
The old version will give you the same counts as the new one.
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On Sat, Feb 25, 2023, 00:53 naila53 ***@***.***> wrote:
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
<#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..
[image: image]
<https://user-images.githubusercontent.com/56326205/221341004-475a0061-210e-41c5-af06-2c88a47cb257.png>
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naila53
commented on July 26, 2024
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? :(
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Hoohm
commented on July 26, 2024
This is related to the python version.
I think it has to be under 3.6 to fix that
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On Sat, Feb 25, 2023, 12:34 naila53 ***@***.***> wrote:
thank you so much for your prompt response! I tried reinstalling the older
version 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!
[image: image]
<https://user-images.githubusercontent.com/56326205/221371131-8e1dd403-2a08-407c-bd84-e0b6efdefd52.png>
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naila53
commented on July 26, 2024
yes, it is! installed python 3.7 and worked! thank you so much!
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Related Issues (20)
- Percentage unmapped: 100 HOT 18
- Complex whitelist HOT 2
- 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.
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