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I would like to align 150 bp paired-end reads with Bismark v0.23.1. I use a HPC cluster with SLURM. I got this error in align process:
```
Bowtie 2 seems to be working fine (tested command 'bowtie…
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Hi there,
Attempting to use methylation extractor on an aligned WGBS bam file. I keep getting an error that
bismark_methylation_extractor --cytosine_report --bedGraph --genome_folder /WholeGenome…
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Hi Felix !
I think, we identified one of the bugs in the alignment report. I am mapping bisulfite reads to Arabidopsis thaliana (TAIR10) genome and this is the alignment report
```
Bismark rep…
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Hi,
thank you for a very convenient and easy to use tool!
I work with plants where, apart from CpG, CHH and CHG motifs are also common for 5mC modifications.
Would it be possible to have the…
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Hi Felix,
I hope you are doing well. I am using the bismark v0.22.3. I have a question regarding the **MAPQ score for the perfectly mapped reads**. The MPAQ for one read is 40, and the other is 0, …
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Hello,
I'm getting an error when I attempt to build the conversion table using HISAT-3N. I have a sorted SAM file for a paired-end Bisulfite-seq sample from the eGTEx project. My command looks like…
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Hello, and thanks for creating a great tool!
We used TrimGalore to trim shotgun metagenomic datasets sequenced on NovaSeq with the ThruPLEX library prep. We noticed that after trimming with the aut…
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Hello~
I have been working on a WGBS dataset with ~400M reads per sample (post-trimming), PE150bp. For 6 out of 10 samples I achieve a pretty good mapping efficiency (67-78%), but for the rest I ha…
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The process fails at the get_software_versions.py.
The setup is on a cluster. The conda environment is as listed in the `environment.yml`. Depending on the attempt to run, either no results are…
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Hello, I cloned the workspace and got this when I began a workflow: ![71005915-7D9F-4C3C-8EFC-58E8099A4849](https://user-images.githubusercontent.com/5053928/127365709-9b519af3-c80a-42bb-8b5f-2dbad68c…