User: vmicrobio

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vmicrobio240
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Posts by vmicrobio

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Answer: A: How to download all the genome sequences (including draft and complete) of a par
... I'll try something like this: /../edirect/esearch -db nucleotide \ -query "Xanthomonas[organism] AND genome[title]" \ | /../edirect/efetch -format fasta > allXanthomonas.fasta then makeblastdb -in allXanthomonas.fasta -parse_seqids -dbtype nucl -title xanthomonas -o ...
written 11 days ago by vmicrobio240
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Comment: C: How can I make a .bed file from my fasta?
... are your sequences located on the genbank? if so, you can retrieve genebank files and execute a script such as : #!/usr/bin/env python # encoding: utf-8 """ bed_from_genbank.py grab the gene records from a genbank file (edit for other record types). - requires ...
written 4 months ago by vmicrobio240
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Comment: C: idxstats non mapped reads
... that's pretty clear, thanks! ...
written 6 months ago by vmicrobio240
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Comment: C: Create a custom exome .genome for IGV
... so in order to do high throughput there is no ways to do it using command lines? ...
written 6 months ago by vmicrobio240
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idxstats non mapped reads
... Hi, I'm doing alignment using bwa, trying to determine if sequences are mapped or not to a reference. I tried to compare fastq files to one reference and obtained my output in csv using samtools idxstats. I got this output: AE005174.2 5528445 2080495 6121 * 0 0 92628 and do not understand ...
idxstats alignment samtools written 6 months ago by vmicrobio240 • updated 6 months ago by Devon Ryan88k
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Answer: A: Downsampling dataset with more than 60 million reads
... you may try something in awk : cat file.fastq | awk '{ printf("%s",$0); n++; if(n%4==0) {printf("\n");} else { printf("\t");} }' | awk -v k=8000 'BEGIN{srand(systime() + PROCINFO["pid"]);}{s=x++ "downsamp-file.fastq"}' ...
written 8 months ago by vmicrobio240
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Comment: C: conversion of GFF3 formate to BED format
... try this : [https://www.biostars.org/p/61386/][1] [1]: https://www.biostars.org/p/61386/ ...
written 8 months ago by vmicrobio240
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Answer: A: database for reference genome
... Hello, You may retrieve your reference genomes using esearch, with something like this: .../edirect/esearch -db nucleotide \ -query "name_of_your_organism[organism] AND genome[title]" \ | .../edirect/efetch -format fasta > references.fasta ...
written 8 months ago by vmicrobio240
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Comment: C: Read a fasta file | Java
... you can create a class FastaSequence containing the code above, add a 'getHeader' and 'getSequence' and then return only the sequence for your use ...
written 10 months ago by vmicrobio240
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Answer: A: Read a fasta file | Java
... Hi ozdavidd, you may try this : private void readFastaFile(File fastaFile) { InputStream flux; String line; try { flux = new FileInputStream(fastaFile); InputStreamReader lecture = new InputStreamReader(flux); BufferedReader buff = ne ...
written 10 months ago by vmicrobio240

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