User: DNAngel
DNAngel • 60
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Posts by DNAngel
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... I saw that one. My bad. ...
written 6 months ago by
DNAngel • 60
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... 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 ...
written 6 months ago by
DNAngel • 60
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... 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
DNAngel • 60
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... 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
DNAngel • 60
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... 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 ...
written 9 months ago by
DNAngel • 60
• updated
9 months ago by
Pierre Lindenbaum ♦ 129k
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... It worked! Thank you :)
...
written 9 months ago by
DNAngel • 60
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... 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 ...
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... Have you solved this? I am also trying to do the same with no luck :/ ...
written 10 months ago by
DNAngel • 60
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... 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
...
written 10 months ago by
DNAngel • 60
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... 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
DNAngel • 60
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