Closed yifnzhao closed 2 years ago
Hi Yifan,
I think it could be an issue with either the GC correction that failed or noise in the bulk sample. I would suggest to try the following to alternatives:
Please try to run the new nonormal
version of CHISEL, which does not require any matched normal sample (still requires phased SNPs though). If you install the most-updated version of CHISEL, you should be able to read the details of the command by running chisel_nonormal -h
. Also, the interface of the command should be the same as the default chisel
command but you simply do not input any matched normal sample.
You can try to run the nonormal
version of CHISEl also disabling the GC correction by adding the flag --nogccorr
Please let us know how these solutions look like and we can suggest further
Hi Simone,
Thanks for your suggestions. I tried both nonormal
and nonormal
with --nogccorr
modes, and I think the adjusted read depth profile looks much more reasonable to me now.
The RDR plots are below (top= nonormal
, bottom= nonormal --nogccorr
):
Wonderful! Since the results are very similar, I would keep GC correction activated (even though GC bias might be relatively limited within 5Mb bins).
Also, I would try to adjust the paramters for clone identification given your lower number of cells, please see the instructions in the Reccomendations section.
I will close the issue for now, but please feel free to re-open it in case of further issues.
Hi Simone,
When running chisel_nonormal
for one of my samples (around 100 cells), I encountered the following error at the art_illumina
step:
[92m[2023-Feb-23 04:25:14]BAM has been identified as paired-end sequencing with read length 151 and fragment size 344 (sd: 248)[0m
[92m[2023-Feb-23 04:25:14]Simulating sequencing reads[0m
[91m[2023-Feb-23 04:25:14]ART Illumina simuation of sequencing reads failed:
====================ART====================
ART_Illumina (2008-2016)
Q Version 2.5.8 (June 6, 2016)
Contact: Weichun Huang <whduke@gmail.com>
-------------------------------------------
None
[0m
The full error message can be found here.
Thanks, Yifan
Hi Simone,
I tried to run CHISEL on my scWGS dataset (0.5x, ~100 cells, 5Mb bins) with matched blood bulk sample (15x). Somehow the RDR profile and copy number calls are much noisier compared to BAF profile.
Below are RDR and read count (per 5Mb bin) tracks of a representative cell, extracted from CHISEL's output (calls.tsv). I think there might be some problem in the RDR normalization step and am wondering whether you have suggestions on how to fix it. Thanks!
Yifan