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Hello, I have installed clinker with conda create -n clinker -c conda-forge -c bioconda clinker-py
I have try to update to v0.0.28 because I have some errors when I want to compare some genomes:
but…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): v1.2.9
- OS name and version (`lsb_release -ds`): Red Hat Enterprise Linux release 8.5 (Ootpa)
**To Reproduce**
Exact bcbio comma…
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Dear colleagues,
despite trying different formats, inputs and combinations of options, rsem-plot-transcript-wiggles keeps failing with this message:
Transcript/Allele IDs in the expression file is …
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Hi Alex,
I am a beginner with bioinformatics, and I am using STAR aligner 2.7.0 to align a 8000bp viral genome to RNA-seq fasta reads. I have 106 patient samples, and to map one read it has taken m…
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I've experienced a memory leak when using the python `mappy.Aligner` when initialized with a sequence file/FASTA (this is within [Megalodon](https://github.com/nanoporetech/megalodon)). This same memo…
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Hi!
When I use minimap2 in Geneious (minimap2_macos -x map-ont --frag=yes --secondary=no -a ref.fasta query.fasta -o output.sam) or with the command line (minimap2 -x map-ont --frag=yes --secondary=n…
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Hi,
Thank you for continuing to develop ORFik!
```
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS
ORFik_1.22.2
```
It was observed …
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Hello I used coverM to calculate relative abundance of MAGs across metagneomic libraries with the following parameters:
coverm genome -1 *_1.fastq.gz -2 *_2.fastq.gz -d MAGs -x fa --dereplicate --d…
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Hi, Dr. Xu. I have been trying to use CHALM to acquired ajusted methylation levels of promoters. CHALM is tested on python 2.7, my python version is 3.8. To run the script in python 3.8, I make some …
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Hi,
Thanks for this super nice method and the pipeline. In the minimap2 bam outputs, I don't see any junction reads even though minimap2 is run with the `-x splice` parameter. Sashimi plots are all…