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Comment: RNA seq analysis
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prifa
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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 …
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> 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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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…
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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…
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> 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.
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Interestingly, when I didn't provide the adapter file, the number of unpaired forward reads was significantly reduced:
TrimmomaticPE…
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> but then if you only allow to map uniquely mapped reads, you are losing spike-in information,
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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…
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The " missing is because of a copy-paste error in the post..
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and if I use the command as such:
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umi_tools extract --extract-method=regex --error-correct-cell \
--bc-pattern2='(?P…
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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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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…
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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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Did you try https://mib-jouline-db.asc.ohio-state.edu/#introduction ?
>The database can also be accessed via the API. The same API points …
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