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Recent Replies
Comment: Too many unpaired forward reads found by Trimmomatic
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SilhouetteQ
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Using fastp, I found that the adapter sequence for the forward read is corresponding to Trans2_rc in the NexteraPE-PE.fa, while for the re…
Comment: cellranger error message
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Max
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I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
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@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
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> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
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I think this is useless, in the gatk doc:
> For each variant, the tool will look for the target coordinate, reverse-complement and left-al…
Comment: Too many unpaired forward reads found by Trimmomatic
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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`…
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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`.
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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.
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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
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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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dthorbur
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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…
Comment: Too many unpaired forward reads found by Trimmomatic
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GenoMax
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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.
Comment: Too many unpaired forward reads found by Trimmomatic
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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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