bgspiegl / gcparagon Goto Github PK

Hello @BGSpiegl ,
Thanks for developing this great tool. I get the output without errors but if I try to use the -ob parameter to get the tagged bam file, I get the following error (I tried with several different samples):
Traceback (most recent call last): File "miniconda3/envs/GCparagon/bin/gcparagon", line 8, in <module> sys.exit(main()) File "miniconda3/envs/GCparagon/lib/python3.10/site-packages/GCparagon/correct_GC_bias.py", line 3174, in main tag_bam_with_correction_weights_parallel( File "miniconda3/envs/GCparagon/lib/python3.10/site-packages/GCparagon/correct_GC_bias.py", line 2304, in tag_bam_with_correction_weights_parallel tagged_scaffold_bam_files_in_order = order_bams(bam_list=tagged_scaffold_bam_files) File "miniconda3/envs/GCparagon/lib/python3.10/site-packages/GCparagon/correct_GC_bias.py", line 2163, in order_bams chrm, strt, stp = Path(bam_nm).name.split('.GCcorr')[0].split('+')[-1].split('-') # chrom-start-stop ValueError: too many values to unpack (expected 3) Continuing to process next BAM file..

What could this be due to? Thank you.

Regards

Hello!

I tried to install GCparagon into my system (Ubuntu 20.04) from a freshly cloned repository using mamba as recommended, but the environment cannot be solved because of package incompatibility. I have also tried the installation using conda with the classic solver and with the libmamba one, resulting in the same issue.
Any ideas on why this might be happening?

Thanks in advance,

Rocío

Hi,
It's nice to see your work GCparagon to perform GC bias correction at fragment level. However, the required genomic region preselection files are only provided for hg38. This is not applicable to many cases that use hg19 reference genome.

So I tried my best to generate ones for hg19. But I found it's difficult to use the corresponding scripts to do such a work. Could u help generate hg19 ones kindly?

Thanks.