User: madkitty

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madkitty580
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Canada
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Posts by madkitty

<prev • 195 results • page 1 of 20 • next >
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Comment: C: BWA batch script does not execute
... Thank you, will give it a try with your advices. ...
written 2.8 years ago by madkitty580
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Comment: C: BWA batch script does not execute
... Yes I followed the advices there. ...
written 2.8 years ago by madkitty580
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Comment: C: BWA batch script does not execute
... The script is just not doing anything, no files are being creating. ...
written 2.8 years ago by madkitty580
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BWA batch script does not execute
... I'm running an alignment with BWA on multiple exomes files on our server. For some reason it does not output anything, and doesn't even seem to be working... any clue why ?!?! #!/bin/bash #PBS -l nodes=2:ppn=8 #PBS -l walltime=5:00:00 #PBS -N my_username cd $PBS_O_WORKDIR ...
bwa written 2.8 years ago by madkitty580 • updated 2.8 years ago by Brice Sarver2.5k
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Comment: C: How to align 100 samples with BWA?
... Oh good to know that I can start aligning 100 exoms at once ! So would my original script work? for i in $(ls *.fastq) do bwa aln -f input.sai -t 3 hg38.fa ${i%.fastq} done ...
written 2.9 years ago by madkitty580
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Comment: C: How to align 100 samples with BWA?
... It's a hospital server with lots of cores available, that's all I know. What does "1 3" mean in this example? Does it execute file 1 to file 3 then stops or does it tell it to do 3 files at a time??? I usually write a script.sh file and qsub it to the server, smth that looks like #!/bin ...
written 2.9 years ago by madkitty580
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Comment: C: How to align 100 samples with BWA?
... Thanks! Can you explain what do values do in (seq 1 3)? From my understanding it will be aligning from exome 1 to 3. Since we have 100 exomes in total, the goal here is to launch a script that will do the job by itself so I don't need to generate 33 different script, I'm not sure the job will be do ...
written 2.9 years ago by madkitty580
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Comment: C: How to align 100 samples with BWA?
... for i in $(ls *.fastq) do bwa aln -f input.sai -t 3 hg38.fa ${i%.fastq} done Would that work? ...
written 2.9 years ago by madkitty580
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Comment: C: How to align 100 samples with BWA?
... Thank you, Our files have a very generic name from 1 to 100, my question is how do I write these 3 lines in a batch loop? ...
written 2.9 years ago by madkitty580
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Comment: C: How to align 100 samples with BWA?
... Thanks though I am not a computer person and really I don't understand what Snakemake does nor how it does it. :(( How can I apply this to my 100 exoms? ...
written 2.9 years ago by madkitty580

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