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Hi Christa,
Thank you for developing CelFiE. I am trying to run CelFiE on 2 samples (adult normal lung tissues-WGBS). After getting the coverage file from Bismark, I ran your prepare_bismark.sh scr…
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I've run into an error when attempting to run the Nextflow pipeline, so thought I'd reach out in case it's something you've encountered and can quickly identify what might be causing it. Some of the o…
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bash-4.2$ bio-fusion \
> -r1=$R1 \
> -r2=$R2 \
> -transcript=$transcript
I1104 12:57:44.433680 11841 main.go:336] Start reading geneDB
I1104 12:57:44.556241 11841 gene_db.go:310] Reading tran…
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Hello, Thank you for the great pipeline!
Now, I try to run the pipeline to call SV. I get an error when trying to run sv_pipeline.cwl, the error as below:
```Shell
cwltool /home/liuhui/ctDNA-pipeli…
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GATK version: gatk-4.2.3
I have two bam files: `Tumor.bam` is cfDNA data, and `Normal.bam` were reads from white blood cells.
There's a variant C to G at `chr7:116795782` (hg38), I can get this …
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Hi All,
Maybe I missed something but are there a command in snakemake file to specify a sample-paired normal control in the snakemake file? I successfully run once in tumor only mode.
Thanks.
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This is something I've been doing off-bcbio for quite a while and I think it would be worthwhile to streamline. I would like to use this issue to collect information on how people have been doing thei…
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## Bug Report
Similar to #1115 (now fixed), MergeBamAlignment breaks on non-paired input.
Input is a SAM file with both, paired and non-paired reads.
### Affected tool(s)
MergeBamAlignment
…
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@lh3 I was playing around with this tool but I couldn't get it to work on a "simple" case. I duplicated a read 100 times and would expect it to output the duplicated read. Any thoughts?
```
@M…
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Hi, it is a good work!
I hvae done the step1-4 sucessful, but what is the *WGS.FinaleMe.mincg7.mergerd.cov.37.bw. I can't see the file from where.
"ls ***WGS.FinaleMe.mincg7.merged.cov.b37.bw** …