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License: MIT License
Is the QC already working with mm10? In the run_ataqc.sh script I saw the comment that so far only hg19 is working. When I try to run the pipeline with the QC turned on I always get the Error " Genome file %s is not existing".
Thank you for the support.
Hi
I noticed in line 430. when get the count of bam, you shift_width to center the read on the cut site
bam_array = bam.array(tss_ext, bins=bins, shift_width = -read_len/2, processes=processes, stranded=True)
But when I check the paramter in metaseq document, it said
shift_width : int
Each item from the genomic signal (e.g., reads from a BAM file) will be shifted shift_width bp in the 3’ direction. This can be useful for reconstructing a ChIP-seq profile, using the shift width determined from the peak-caller (e.g., modeled d in MACS). Not available for bigWig.
In my opinion, the shift_width is based on the single_end and short read length. But now, almost all sequencing is PE 150. So is it necessary to set the paramter?
By the way, I found whether set the paramter will make a great influence on the result. If I set the paramter, the TSS enrichment will be 6 while drop the paramter, my enrichment will be 4.
And the 4 is same as my own R script calculated TSS enrichment.
If I'm not mistaken, the scritpt run_ataqc.py
is broken due to a change of API in samtools sort
, notably lines 522 and 524.
See samtools 1.3 release:
The obsolete samtools sort in.bam out.prefix usage has been removed. If you are still using ‑f, ‑o, or out.prefix, convert to use -T PREFIX and/or -o FILE instead.
Could be nice to document this version constraint or would you be accepting a patch to update the script?
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