Haibo Liu
Haibo Liu
I found the same error. Could the developer give some comment? Thanks, Dr. Yu.
Hello Wenbao, Thank you for your quick response. I did run like that. But the integrate module seems not to perform all downstream analysis. So I ran downstream after integration,...
Thank you, Wenbao, for the instructions. One question is how I should provide an scATAC-pro-aware BAM file for the merge experiment for downstream analysis. Do I need to manually merge...
Thanks again, Wenbao. I think I need to run all the steps except "split_bam" after integration. By the way, does the pipeline remove duplicates in the final filtered, sorted BAM...
Got it. Thank you. Haibo On Tue, Aug 23, 2022 at 11:52 AM Wenbao Yu ***@***.***> wrote: > The duplicates were not removed from the bam file. (But note that...
I encountered the same problem. It works for me when the BAM file coming from 35-bp read alignment, but not for BAM file coming from 100-bp read alignment. I think...
the two lines: https://github.com/nf-core/cutandrun/blob/3.2.2/modules/local/for_patch/trimgalore/main.nf#L18-L19, are wrong with missing commas. you also need to remove the empty line, see follows. output: tuple val(meta), path("*trimmed.fastq.gz") , emit: reads tuple val(meta), path("*report.txt") ,...
@jdrnevich, the bug should have been fixed.
Oh. That's a typo. I just corrected it. Thank you. Haibo On Fri, Mar 14, 2025 at 1:21 PM Ana (Howells) Ferreira < ***@***.***> wrote: > Hi dev team, >...