Wenbao Yu
Wenbao Yu
You can process each sample using `process` module first, followed by `integrate` module.
Hello Haibo, Oh, the `downstream` module was designed for each sample, not for a integrated object. You may need to run the exact module, like the clustering and motif_analysis separately...
Thanks. I am not sure. I haven't used scATAC-pro with merged bam file for integrated data. Which specific step within downsteam module do you want to run? You don't have...
The duplicates were not removed from the bam file. (But note that we only use unique fragments in scATAC-pro analysis.)
Hi Haibo, thanks for pointing out this issue. Since this only matters in a very few situation (like footprint analysis), I made the shifting be done optionally by turn a...
I am not sure but maybe you can check out in this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6203779/ If you are not specifically interested in the % of reads mapped to promoter or enhancer,...
Can you check the log file for any warning or error? Also, check anything abnormal in your trimmed fastq files. Usually, it needs large memory for the mapping step (at...
Thanks for pointing it out and we will try to improve it for future release. The demultiplexing step is slow but not to that extend as you mentioned(should be also...
I'm not sure if no further information. Have you tried run *integrate* module instead of breaking it into 3 steps? or may need to increase the gap from 200bp to...
220k seems good to me! Thanks.