[--i5 STRING] [--i7 STRING]

[sandberg-lab]

[--i5 STRING] [--i7 STRING]

[AntonJMLarsson]

If your sequencing data is not dual indexed I don't recommend my software. If your experiment is single indexed with UMIs (like eg 10x) consider this software instead https://csglab.github.io/PhantomPurgeR/

[AntonJMLarsson]

Hello,

Given that each row corresponds to a sample, the --i5 and --i7 parameters specify the cell barcode for the i5 and i7 adapters respectively. Please look in the README for an example. If your data is in the other configuration (i.e. each column is a sample), you can specify this with the --column option.

Let me know if you have any questions.

Anton

[Samaneh14]

Hi Anton,

Thanks for your answer. Yes, indeed the matrix consists cell barcodes as columns and genes as rows. I set the run command by ./unspread.py matrix.csv --column 1

However, it still gives the following:

Reading file: matrix.csv
Traceback (most recent call last):
File "./unspread.py", line 69, in
df = df.sort_values(by=[i5_index_name,i7_index_name], ascending=[False, True])
File "/miniconda/envs/python3/lib/python3.9/site-packages/pandas/core/frame.py", line 5442, in sort_values
keys = [self._get_label_or_level_values(x, axis=axis) for x in by]
File "/miniconda/envs/python3/lib/python3.9/site-packages/pandas/core/frame.py", line 5442, in
keys = [self._get_label_or_level_values(x, axis=axis) for x in by]
File "/miniconda/envs/python3/lib/python3.9/site-packages/pandas/core/generic.py", line 1684, in _get_label_or_level_values
raise KeyError(key)
KeyError: 'i5.index.name'

Should I adjust i5 and i7 in addition to --column 1?

Best regards
Samaneh

[AntonJMLarsson]

Hello,
Yes, you need to change them to the actual name of the rows which have the i5 and i7 indexes.

Best,
Anton

[Samaneh14]

Dear Anton,

How may the code be adapted for the libraries with just cell barcodes and UMIs, when the i5 and i7 adapters are lacked?

Thanks in advance for your time.

Regards,
Samaneh

[Samaneh14]

If your sequencing data is not dual indexed I don't recommend my software. If your experiment is single indexed with UMIs (like eg 10x) consider this software instead https://csglab.github.io/PhantomPurgeR/

Dear Anton,

Thank you so much for the comment. Great solution.

Best regards
Samaneh