Open MohammadIzadi opened 9 months ago
Hi @MohammadIzadi
Can you show the head of your fragments file?
Best,
Seppe
Hi @SeppeDeWinter,
Many Thanks for your response. I attached my fragments file in this comment. Thanks again for your help.
Best,
Mohammad
Hi @MohammadIzadi
Can you also provide the full function you were running (with all parameters).
For the fragment file, I see that the 5th column is all 0. The column represents "the total number of read pairs associated with this fragment. This includes the read pair marked unique and all duplicate read pairs." (see https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments) so 0 does not make a lot of sense.
Best,
Seppe
Hi @SeppeDeWinter
Thanks for your response. I attached wrong fragments file and I upload it again. I convert anndata to fragments.tsv file and now I delete rows that have zero values. I attached again fragments file in this comment. I get screen shot from consensus_peaks and compute_qc_stats() parameters and I attached them. consensus_peaks variable have only one row. Is it correct? fragments(1).tsv.gz
Hi @MohammadIzadi
Having only a single consensus peak is not good! Something went wrong there.
Also I would not delete all rows with a zero count for your fragments file (probably the number 0 is wrong). Could you specify how exactly you generated your fragments file? The fragments are also quite long (5kb). A typical fragment size distribution looks like the plot below
(from ArchR).
Best,
Seppe
Hi,
Thank you for developing SCENIC+. I am excited to use it. When I want to use compute_qc_stats(), I get below traceback.
Can you help me to fix it, please? Best,