User: DNAngel

gravatar for DNAngel
DNAngel60
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5 months, 3 weeks ago
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3 years, 3 months ago
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k********************@hotmail.com

Posts by DNAngel

<prev • 83 results • page 1 of 9 • next >
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Comment: C: How to loop over multiple files for BWA MEM in bash for loop?
... I saw that one. My bad. ...
written 6 months ago by DNAngel60
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(Closed) How to loop over multiple files for BWA MEM in bash for loop?
... Hi all, I've written a large bash script for single-end paired reads which uses bwa mem. It works great. But now I have a new dataset that is paired-end and the only part I need to change is the beginning where bwa mem uses a reference file and sample files to align them. I cannot figure out how to ...
bwa bash written 6 months ago by DNAngel60
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Comment: C: Optimize bwa mem in parallel on a SLURM cluster
... How would you modify this if you have many reference files to process for many fastq files? If my reference.fasta files are saved in a large list in reflist.txt, and I have another directory with my fastq files to process how does one instead use parallel to process many reference.fasta files simul ...
written 9 months ago by DNAngel60
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Comment: C: How to parallelize bwa mem for single-end data within a larger bash script?
... I know but because I have multiple fastq ffiles to process for 1000s of ref genes (which the link you provided and others I've found here do not have this problem) I am unsure which part of my script to change. Do I use parallel to call the individual REF files of which I have thousands and in that ...
written 9 months ago by DNAngel60
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How to parallelize bwa mem for single-end data within a larger bash script?
... I've seen some posts here that have tried to parallelize bwa-mem for their sample data but all examples were paired-end data and the code was standalone (i.e. they only needed it for bwa mem and maybe converting SAM to BAM). But I also have to run my script for 1000s of different reference files and ...
bwa-mem gnu-parallel bash written 9 months ago by DNAngel60 • updated 9 months ago by Pierre Lindenbaum129k
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Comment: C: How do you extract longest transcript from fasta file using length and header ID
... It worked! Thank you :) ...
written 9 months ago by DNAngel60
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How do you extract longest transcript from fasta file using length and header IDs?
... Here is an example file that I made up to practise and it is called Medaka_TEST.fa where the header is GENE_ID | TRANSCRIPT_ID: $ cat Medaka_TEST.fa >ENSORLG000000000AA|ENSORLT000000000AD # This gene has two transcripts (next sequence) KEEPTHISONETHISISTHELONGEST >ENSORLG000 ...
fasta awk written 9 months ago by DNAngel60 • updated 9 months ago by JC11k
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Comment: C: Generate Consensus sequence from BAM file
... Have you solved this? I am also trying to do the same with no luck :/ ...
written 10 months ago by DNAngel60
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How to loop over a directory to set each file as a variable?
... Hi all, I have a bash script that I can call and I supply command line arguments to feed specific files into it. It works fine, but I want to optimize it but looping over a new directory where each file is set as a new argument. For example my script below: #!/bin/bash REF=$1 NAME=$2 ...
bash written 10 months ago by DNAngel60
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Comment: C: Does Abyss work on single-end Illumina reads only?
... Ah okay I thought -se would be for single-end as well but it does say it requires a short and a long read assembly which I do not have. That's unfortuante! ...
written 10 months ago by DNAngel60

Latest awards to DNAngel

Scholar 20 months ago, created an answer that has been accepted. For A: How to save trimmomatic terminal summary to an output file?

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