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Hi,
I am currently engaged in a research project focused on the methylation genome of Crocus sativus. Unfortunately, a reference genome is not yet available for this species. Consequently, we have …
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Hi, thanks for this fast and easy-to-run aligner :) I have two questions.
1. How the "coverage" in the report was calculated? I had a coverage value 0.95 from a human GRCh38 to human T2T alignme…
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chkRefFiles is searching for folder ending in ".Idx" but the make-index function for hisat2 names it with a dash "genome-hisat2Idx". Also bwa doesn't appear to make any such folder. Thus I've only tes…
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PEPATAC with looper failed with the latest looper and eido
here is the error message:
```Looper version: 1.4.0
Command: run
/home/bx2ur/.local/lib/python3.8/site-packages/divvy/compute.py:150…
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**Version info**
- bcbio version 1.2.9:
- OS Ubuntu LTS 20.04:
**To Reproduce**
Exact bcbio command you have used:
```
bcbio_nextgen.py ../config/CTRL-MDD-S-MDD.yaml -n 72
```
Your yaml …
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I tried wit 700 Mbp genome and got a fantastic results! Thank you!!
Now I'm now working on a plant genome of ~4 Gbp and got segmentation fault problem.
So if it is using too much memory, is there …
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### Description of the bug
The error appear when nf-core/scrnaseq is launched with any aligner at the emptydrop step. The pipeline is labelled as completed but with errors as it failed with the outp…
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Hi there,
I'd like to try using circompara2 to map circRNA reads in human genome for my RNAseq project. But since my project has over 1000 samples and we've already done the alignment work for mRNA b…
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As we use splice aware aligner "Hisat2" to align our reads based on whole genome or even with specific chromosome (15) we found that the overall alignment of all reads approximately 5% .
This low ali…
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Hello dear developers,
I am using PECAT to assemble a diploid genome (SMRT Cell, PacBio), however, the process is stuck at the assembly stage, the following error appears:
```
2024-07-31 11:0…