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I have the sequencing data in Nanopore of a small amplicon (230 bp) of the HLA-C gene. One of the challenges I face is the low quality of the sequences obtained, as well as the fragmentation of the se…
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Hello!
I’m using Bismark to analyze whole genome EM-seq and targeted BS-seq (after the bisulfite conversion the region of interest is amplified before the sequencing). For both the experiment I have …
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Hi @FelixKrueger
I had a question - more of a thought process - regarding deduping the fastq sequences before it reaches the aligner.
http://felixkrueger.github.io/Bismark/bismark/library_type…
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Hi!
I have been trying to use methylkit for Bisulfite Sequencing samples. Finally I have achieved the differentially methylated regions list with the %methylation value and I would like to know if it…
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### Description of the bug
Hi, I run the pipeline with profile test but it shows the error as follows:
```
Command error:
[ERROR] Please provide a valid value for --ena_metadata_fields!
Pro…
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Hi team,
I ran WGBS workflow with publically available WGBS dataset and met an error.
I checked the issuses but couldn't find same error I met.
Below, I attached the logs.
Thank you for your h…
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### Description of the bug
Over the past few days I have encountered an issue when running `nextflow run nf-core/fetchngs`that is related to the accepted values for `--ena_metadata_fields`. No change…
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The [ENA API changed yesterday](https://docs.google.com/document/d/1RPHmK8Pvm9UxSa21Ej3MkGoGYO9baSxwxk_dOuWWyNE/edit?usp=sharing) and the following fields are no longer valid: `cram_index_ftp,cram_ind…
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Hello,
for methylation outputs, what is "CpGx" as a methylation site category?
Thank you.
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Hello,
Single-end read IDs are generated correctly, but when generating paired-end reads with
```
(bioitools_dev) gzynda-mbpr:BSMAPz gzynda$ perl Sherman -l 100 -n 2 --genome_folder ./genome/ -…