Moderator: Jorge Amigo
Jorge Amigo ♦ 12k
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- Santiago de Compostela, Spain
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- Joined:
- 10 years, 7 months ago
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Scrutinizing genomic human variation by dealing with high throughput genotyping and next generation sequencing results, among many other things.
Posts by Jorge Amigo
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... Fair enough, Ram. I was just surprised how anyone could think that the best way to get his first p-value knowledge would be to post a question in a bioinformatics forum rather than performing a simple google search to read the first 2-3 results. Anyway, I'm also surprised how such basic question hav ...
written 8 days ago by
Jorge Amigo ♦ 12k
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... I would definitely go for @ATpoint's samtools solution in general, as it should work always and it should be really fast.
If programming alternatives like @i.sudbery's awk solution in general or @jenn.drummond's grep if your fasta file is linearized would be considered, here is a perl alternative j ...
written 13 days ago by
Jorge Amigo ♦ 12k
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... Very interesting. I had never thought about using awk's record and separators like this to split files having grouped lines. ...
written 13 days ago by
Jorge Amigo ♦ 12k
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... Pierre's answer would still work. It'll output columns 4, 1-3 and 5 of the first file, plus 1-3 and 5 of the second file. As Pierre mentioned, you may modify the column layout using the `-o` option. [Here][1]'s an example that may help you understand hoy join output format works.
[1]: https://sh ...
written 17 days ago by
Jorge Amigo ♦ 12k
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Answer:
A: editing gtf file
... Here is a perl one-liner that would do the job:
perl -pe 's/gene_id ""; transcript_id "([^"]{1,10})/gene_id "$1"; transcript_id "$1/' input.gtf > output.gtf
The pattern `[^"]{1,10}` matches the first 10 characters of transcript_id, even if its length is shorter. ...
written 19 days ago by
Jorge Amigo ♦ 12k
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... A fasta file is a text file containing sequence information, being sequence ids in lines starting with the '>' character and the sequence itself right after the id. In your example, you have 2 sequences NC_045512.2 and MW326508.1 which use the id line to provide annotation right after the '|' cha ...
written 19 days ago by
Jorge Amigo ♦ 12k
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... If you are completely sure that your sequence database contains pairs of id+sequence lines, you could combine your both greps in 1. You'll get all the IDs that match your query even if they are repeated, plus you'll have all the next-match-line sequences at once, getting the desired results in a sin ...
written 19 days ago by
Jorge Amigo ♦ 12k
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... Good to know. Thank you Pierre. ...
written 29 days ago by
Jorge Amigo ♦ 12k
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... Any pure sorting solution will only work if both files contain the same IDs and nothing else, as it will pair every 2 lines independently on their ID. A previous selection of IDs present in both files should be performed before using this code. Here's an example nesting 2 `cut | grep`, one to detect ...
written 29 days ago by
Jorge Amigo ♦ 12k
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... ... and the simplest I would go for. Considering that `join` output provides the ID in the first column, here's a minimum modification to exactly match the desired output:
join -t $'\t' -1 4 -2 4 <(sort -k4,4 file1.bed) <(sort -k4,4 file2.bed) | perl -pe 's/(\S+)\t(.+)/$2\t$1/' ...
written 29 days ago by
Jorge Amigo ♦ 12k
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For A: Which Version Of Gatk Do People Use
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For A: Check if REF allele is minor allele in any variant
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For A: Check if REF allele is minor allele in any variant
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For A: Which Version Of Gatk Do People Use
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For A: Is It Ok To Use One End Of A Set Of Paired-End Reads As A Set Of Single Reads?
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For A: Which Version Of Gatk Do People Use
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For A: Check if REF allele is minor allele in any variant
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For A: Which Version Of Gatk Do People Use
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For A: Check if REF allele is minor allele in any variant
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For A: Which Version Of Gatk Do People Use
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For A: Filtration of bam file but with header
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13 months ago,
created an answer that was upvoted at least 5 times.
For A: Is It Ok To Use One End Of A Set Of Paired-End Reads As A Set Of Single Reads?
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For A: Is It Ok To Use One End Of A Set Of Paired-End Reads As A Set Of Single Reads?
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For A: Which Version Of Gatk Do People Use
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For A: Filtration of bam file but with header
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