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Hello,
I am using the IGV(2.11.0) to view a region has about 20-30 reads in bam. When I zoom in, it gives me "unexpected error repainting view" error and no reads at all.
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Hello,
I have this error with --parallel and without too.
>>> Writing bisulfite mapping results to S15_R1_001.fastq.gz.temp.1_bismark_bt2_pe.bam A converted versions of the FastQ file S15_R2_001.…
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hello!
Quick question:
I started a run ( a few hours in) and realized that I want to try out the following tags, based on this segment from the documents.
`In addition, the --mod-map-base-conv…
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Dear Felix,
When I extract methylation call from BAM files, it always failed with perl error:
Command:
```
bismark_methylation_extractor -s -o bismark_methylation_extractor_mm9 --gzip --bedGrap…
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Hi @jts,
I hope you are doing well,
In the newer versions of nanopolish, you have implemented a mapping quality of more than 20 during methylation calling. But, as far as I am aware, there is no o…
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Hi, recently I encountered this data covering index not exist error.
The commend I used are:
$megalodon $fast5 \
--guppy-server-path /the/path/ \
--guppy-params "-d /pathto/rerio/basecall_model…
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Hi Yoann,
after updating methview.qc() to version 0.027 and BiocompR to version 0.0.155 (Beta) I tried to run the plot.all.qc() function and the following error occured:
**Describe the bug**
Th…
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Hi Felix!
Not an issue, but I (and I hope many other users) would highly appreciate your recommendations on how to process L phage genome control WGBS data with Bismark.
One of the solutions wou…
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Hi, running Megalodon version: 2.3.4, with Guppy 5.0.7 as the basecall server on a WGS sample generated on a R9 PromethION flowcell.
Command I used:
```
megalodon \
/path/to/fast5/ \
…
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Hello! I have matched bisulfite and oxidative bisulfite paired-end RRBS data from mouse brain which I have processed with TrimGalore and Bismark. The intention was to be able to calculate DNA hydroxym…