User: PedroBarbosa

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PedroBarbosa10
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Location:
Braga, Portugal
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4 days, 6 hours ago
Joined:
6 years, 10 months ago
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Posts by PedroBarbosa

<prev • 7 results • page 1 of 1 • next >
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Comment: C: tabix indexing on a non vcf/bed/sam txt file
... @finswimmer, it didn't work, unfortunately. These are my full commands, if you see any possible source of error let me know. This "wrong" index takes 2 seconds to be created. Never happened before. header_file=$(head -n1 $files) zcat $header_file | head -1 | cut -f1,2,3 | bgzip > fitc ...
written 17 days ago by PedroBarbosa10
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Comment: C: tabix indexing on a non vcf/bed/sam txt file
... Indeed, it worked for my little example. I'm now running a large sort on the file (`sort -V -k1,1 -k2,2`) to see if this was the problem. Although I wasn't expecting that as I zcatted all chromosome files in the proper order, and in theory I donwloaded them already sorted. Thanks for the suggestion ...
written 17 days ago by PedroBarbosa10
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tabix indexing on a non vcf/bed/sam txt file
... Hello, I'm struggling to get the tabix index on a simple 3 columns bgzipped txt file: #chr pos score 1 1 0.061011 1 2 0.061011 1 3 0.061011 ... Oddly, the indexing step is really fast (like 2 seconds), considering the file size (9Gb) ...
software error next-gen written 18 days ago by PedroBarbosa10
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Comment: C: Genomic coordinates from GENCODE annotation file
... How did you make that bed file ? There should be only one gene record in the whole gtf pointing for ISG15. It seems you have all the sub features of the gene in that bed. First line of your file seems to be the whole gene feature, which you would obtain with the command I referred. Edit: Just saw ...
written 5 months ago by PedroBarbosa10
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Answer: A: Genomic coordinates from GENCODE annotation file
... You can look in your 3rd column of the GTF file for gene records and create a bed out of it. Then, you extract the variants in those regions using bcftools/bedtools/etc awk -v OFS="\t" '$3 == "gene" { print $1,$4-1,$5,".",".",$7 }' gencode.gtf | bedtools slop -s -r 0 -l 5000 -i stdin -g genome ...
written 5 months ago by PedroBarbosa10
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Comment: C: How To Instantiate A Sequencdb Class For Use In The Seqsimilaritysearcher Interf
... That was exactly the implementation that i was following to perform my search but it is a old one and some classes and methods could not be used. Anyway i started writing an implementation by my own not using biojava , instead calling the commandline blastp that i've installed in the system. That ...
written 5.8 years ago by PedroBarbosa10
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How To Instantiate A Sequencdb Class For Use In The Seqsimilaritysearcher Interface Of Biojava
... I'm trying to run blastp using some biojava packages. I realized a class that can perform BLAST searches should be implementing the Interface SeqSimilaritySearcher from the package org.biojava.bio.search. Unfortunately, i need to give a SequenceDB to this method. I want to do the search on protei ...
biojava java database written 5.8 years ago by PedroBarbosa10 • updated 5.8 years ago by Istvan Albert ♦♦ 79k

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