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Hi there,
Just wanted to say great paper, its fantastic that you can push the throughput by optimizing the decrosslinking.
I am currently using Pore-C but adapted using DNase based method to fra…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.2.9
- OS name and version (`lsb_release -ds`): Ubuntu 22.04 LTS
**To Reproduce**
Exact bcbio command you have used:
```
bcbi…
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Hello,
I'm trying to RNAseq pipeline on canine ref genome as below. But get the error. Wondering - if it has to do with as s3 permission issues.
```
nextflow run nf-core/rnaseq -r 1.4.2 -profi…
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### Description of the bug
I am trying to run nf-core with RSEM to quantify gene expression.
However, the process RSEM calculate expression fails and exits with error code 255.
Upon inspection of…
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Hi Felix,
I have recently started using Bismark (version 0.23.0) and have compared the output to another pipeline (BSMAP+MethylDackel). I get very different results between the two pipelines and I …
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Hi,
I am trying to process a couple of single end fastq files, however, STAR aligner is throwing a Bus error
```
/bin/bash: line 16: 99885 Bus error STAR --runMode alignReads --r…
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I like that SNPs are represented on a linear scale even on log plots (because, for example, it's really confusing to see a SNP at 50% frequency that is almost at the top of a graph), but the total gra…
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It looks like the core implementation of process_bam should easily be applied to sam files too. The CIGAR string and alignment position need to be modified (implemented properly).
Helpful links:
Expl…
kclem updated
2 years ago
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I've been trying to hunt down where this is happening in [the template](https://github.com/bcbio/bcbio-nextgen/blob/v1.2.8/bcbio/workflow/template.py) but not getting anywhere. Any suggestions? I'm ha…
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## Short description of the problem
"anvi-self-test --suite pangenomics" runs, but with lots of errors. Is it worth going through it?
also tested instructions for
"A real example for committed…