User: valastesolutions

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Posts by valastesolutions

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Comment: C: Bash script problem
... Thanks, I will try the parameter substitution. I am absolutely sure that the BAM file in s$1 contains all reads. I will let you know if this works. Thanks all for your time. ...
written 11 weeks ago by valastesolutions0
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Comment: C: Bash script problem
... #!/bin/bash echo initiating callvar_rna on $1 echo running samtools sort samtools sort $1 -o s$1 echo running samtools index samtools index s$1 echo selecting reads from bedtools intersect -wa -a s$1 -b $2 > KRAS_s$1 ...
written 11 weeks ago by valastesolutions0 • updated 11 weeks ago by Jean-Karim Heriche23k
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Comment: C: Bash script problem
... Hi, in fact I build the script first echoing each line to see if the commands are correct, and in fact they are. I have posted the complete script in replay to the remark below. Any help would be welcome. Steven ...
written 11 weeks ago by valastesolutions0
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Bash script problem
... Hi, I am writing a bash script to call variants in RNA-seq data. At some point, I want to select only ready reads corresponding to a specific genomic region using bedtools intersect and redirect the output to a smaller BAM file more amenable for variant calling. I have used following command for th ...
bedtools bash written 11 weeks ago by valastesolutions0 • updated 11 weeks ago by lieven.sterck8.3k

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