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Hi,
I am a first time user of bismark, and I just wanted to say the documentation you prepared is very clear and helped me immensely. Thank you.
The problem I am encountering might be due to my …
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Hi,
I used bismark to do the alignment, but the 'Mapping efficiency' varies from 19.1% to 48.4%. My reads are pair-end, genome is Oryza Sativa. I read some previous issues and your answers about lo…
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Hi,
Thanks for this amazing tool. I have several questions and would really appreciate it if you can help.
1. What's the difference between the pre-trained models `dna_r9.4.1_e8` and `dna_r9.4.1_e…
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Hi, Jeff,
I have DNA methylation data generated from whole genome bisulfite sequencing. I want to correct unknown batch effect in my data, but encountered error message `Error in eigen(t(resid) %*% r…
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**Describe the bug**
when using `pysradb search -d ena` with the `--strategty` flag, a value containing a dash fails to produce a result.
```
--strategy must be one of the following:
AMPLICON, AT…
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First of all, thank you for developing hisat 3N. As a previous bismark user, I am excited by the rapid alignment capability of hisat 3N and its high mapping efficiency.
Using whole genome BS seq d…
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How can I use hg38 assembly for creating methylkit object? Does it need any specific format (indexes) of the hg38 or regular fasta?
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Hello,
When creating the quality control reports we are noticing for a number of datasets that the bisulfite conversion rate is `N/A` in the HTML QC. We thought it might be due to low lambda covera…
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During read alignment of my single end, directional RRBS data I noticed that ~50% or reads mapped to Watson C2T while ~50% mapped to Crick C2T. However, it is my understanding that reads originating f…
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Hi,
I'm using samtools version 1.9, trying to name sort TCGA bam files and convert them to paired end fastq files.
It works fine for some bam files with this command.
```
samtools sort -n ./f224fd…