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Best way to query VCF for specific variants
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
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Fungal genetics
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Hi, Below SNPEff database building error I am getting. "FATAL ERROR: Most Exons do not have sequences!" The headers are correct and sam…
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Rubayetul
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the last line of SeqIO.write(record.....'fasta') in a for loop will input the the last record into new fasta file and it will only contain …
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You could use `sarek` (nf-core's exome pipeline) if you don't want to customize or reinvent : https://nf-co.re/sarek/3.4.2
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Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
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Two last seats have just become available. Apply now, if you want them.
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
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You always need to add the following option when you are using `-p` to count paired-end reads. --countReadPairs If specified, fragm…
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Hi swbarnes2, that was the problem, they were not numeric but as character columns. converted them and it fixed the error. Thank you for yo…
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
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I figured out: Since featureCounts counts fragments and not reads, we have pair-end data that means **Assigned** value from the output w…
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
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kalavattam
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> My question is this: "mate reverse strand" (flag 16/0x10) or "read reverse strand" (flag 32/0x20) do not directly relate to the strandedn…
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As you stated, your problem is likely division by 0. See this [Cross-Validated][1] post that seems to be very similar to your problem. In …
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Consider using SLURM job arrays if you want to use a `for` loop inside a single SLURM job: https://hpc.nmsu.edu/discovery/slurm/job-arrays/
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Thank you so much dthorbur. Yes I am new to imputation analysis. I will follow your kind suggestions. Thanks again!
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I don't know but another way of doing it would be to combine different datasets of different strains that you know are clonal. Then you kno…
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Please check out these posts https://www.biostars.org/p/367626/
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