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Comment: Question about methylation location
Comment: Question about methylation location
How to use minimap2?
Comment: RNA seq analysis
Comment: Filtering Multi-sample VCF file for all except one Genotype
Truncated metadata file report from ENA Portal API
Comment: Truncated metadata file report from ENA Portal API
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Comment: samtools tview symbols
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Ruqaiya
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What does the star mean then ?
Comment: RNA seq analysis
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prifa
▴ 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
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SilhouetteQ
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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
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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
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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
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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
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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
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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
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Giulia
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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
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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
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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…
Comment: Correlation Analysis
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manaswwm
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If your *gene_corr* data frame contains one gene instead of all genes, then the correlation would be per gene. If your *gene_corr* data fra…
Comment: UMI-Tools knee-method has great influence on the results of white list
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Assa Yeroslaviz
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I think I might know my problem. The barcodes are in this case on read2 and not on read1. Does umi-tools recognise it automatically, or do …
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