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Recent Replies
Comment: Too many unpaired forward reads found by Trimmomatic
by
GenoMax
142k
Ideally you will know which adapters to use but if you don't then programs like `fastp` can auto-detect them. You could also use `bbduk.sh`…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
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With the `--read2-only` option (which isn't available yet on the bioconda version), this will complain about a lack of `--bc-pattern`.
How…
Comment: RNA seq analysis
by
prifa
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10
it's raw data **fastq.gz**, so for example I have 4 different samples from different tissue, sample A with 3 replicates, samples B,C and D …
Answer: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> The goal is to remove all the variants which are unique to the KWSBambina sample.
using jvarkit vcffilterjdk https://jvarkit.readthedo…
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
•
0
The first example used the adapter file NexteraPE-PE.fa, but it generated more than 50% unpaired data......
The content of NexteraPE-PE.fa…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
•
0
Ok so I definitely didn't understand at first what my goal was.
The goal is to remove all the variants which are unique to the KWSBambina…
Comment: Question about methylation location
by
dthorbur
★
1.9k
What data do you have? Generally, you start with sequencing data, which you need to clean and then map to a reference genome. Then dependin…
Comment: Too many unpaired forward reads found by Trimmomatic
by
GenoMax
142k
> when I didn't provide the adapter file
Still see the file here `ILLUMINACLIP:./NexteraPE-PE.fa:2:30:10 `, unless that is an empty file.
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
•
0
Interestingly, when I didn't provide the adapter file, the number of unpaired forward reads was significantly reduced:
TrimmomaticPE…
Comment: Alignment of samples with spike-in
by
GenoMax
142k
> but then if you only allow to map uniquely mapped reads, you are losing spike-in information,
How so? Spike-in's are generally unique s…
Comment: Truncated metadata file report from ENA Portal API
by
GenoMax
142k
While there is no timeout by default on the `get` operation, you may want to set a higher value and see if that helps, since there is a lar…
Comment: Truncated metadata file report from ENA Portal API
by
Giulia
•
0
The " missing is because of a copy-paste error in the post..
I know wget but my tool is entirely in python. I really don't understand why i…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★
1.8k
and if I use the command as such:
```
umi_tools extract --extract-method=regex --error-correct-cell \
--bc-pattern2='(?P…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
No, UMI-tools won't work this out automatically, you'll need to either switch read1 and read2 or use the new `--read2-only` which is curren…
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