Moderator: Jorge Amigo

gravatar for Jorge Amigo
Jorge Amigo12k
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Location:
Santiago de Compostela, Spain
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https://www.researchga...
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Google Scholar Page
Last seen:
11 hours ago
Joined:
10 years, 7 months ago
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a****@yahoo.com

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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Comment: C: What does p-value mean ? What and how can i interpret the results
... 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 Amigo12k
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Answer: A: How to extract a sequence below a fasta header (">") from a fasta file ?
... 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 Amigo12k
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Comment: C: How to extract a sequence below a fasta header (">") from a fasta file ?
... 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 Amigo12k
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Comment: C: how to combine two bed files using the same ID information
... 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 Amigo12k
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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 Amigo12k
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Comment: C: how to parse a .fasta file in python ?
... 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 Amigo12k
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Answer: A: how to filter sequence database with bash?
... 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 Amigo12k
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Comment: C: how to combine two bed files using the same ID information
... Good to know. Thank you Pierre. ...
written 29 days ago by Jorge Amigo12k
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Comment: C: how to combine two bed files using the same ID information
... 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 Amigo12k
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Comment: C: how to combine two bed files using the same ID information
... ... 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 Amigo12k

Latest awards to Jorge Amigo

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 24 days ago, created an answer that has been accepted. For A: Check if REF allele is minor allele in any variant
Scholar 8 weeks ago, created an answer that has been accepted. For A: Check if REF allele is minor allele in any variant
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 9 weeks ago, created an answer that has been accepted. For A: Check if REF allele is minor allele in any variant
Good Answer 10 weeks 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?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Scholar 10 weeks ago, created an answer that has been accepted. For A: Check if REF allele is minor allele in any variant
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 3 months ago, created an answer that has been accepted. For A: Check if REF allele is minor allele in any variant
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How To Analyse Snp Data From Different Sources?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Appreciated 7 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: How To Analyse Snp Data From Different Sources?
Good Answer 11 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?
Scholar 13 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header
Good Answer 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?
Good Answer 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?
Appreciated 14 months ago, created a post with more than 5 votes. For A: Order Of Gatk Commands
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Which Version Of Gatk Do People Use
Scholar 14 months ago, created an answer that has been accepted. For A: Filtration of bam file but with header

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