GRIAC/system_genetics
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WIP: added fastQC code snippet (.pl and .sh scripts) #4

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R. Bults wants to merge 1 commits from p287376/system_genetics:master into master
pull from: p287376/system_genetics:master
merge into: GRIAC:master
Conversation 1 Commits 1 Files Changed 2 +50
R. Bults commented 2021-02-15 16:08:18 +01:00
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Code to perform fastQC on paired-end sequencing data.

Code to perform fastQC on paired-end sequencing data.
R. Bults added 1 commit 2021-02-15 16:08:22 +01:00
R. Bults requested review from J.v.N. 2021-02-15 16:08:45 +01:00
J.v.N. requested changes 2021-02-15 16:12:02 +01:00
rnaseq/step1_fastqc/00_fastqc.pl
@ -0,0 +1,23 @@
#!/usr/bin/perl -w
J.v.N. commented 2021-02-15 16:10:59 +01:00
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Preferably only BASH, and preferably only the main command ;-)

Preferably only BASH, and preferably only the main command ;-)
rnaseq/step1_fastqc/00_fastqc.pl
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my $sample = $file1;
$sample =~ s/\_R1\.fastq\.gz$//;
mkdir $sample.'_R1', 0700;
system join(' ', 'fastqc', '-o', $sample.'_R1', $file1);
J.v.N. commented 2021-02-15 16:11:48 +01:00
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This is the main command, the only thing you need ;-) (As a bash command. This is a system call from PERL)

This is the main command, the only thing you need ;-) (As a bash command. This is a system call from PERL)
J.v.N. commented 2021-02-15 17:07:50 +01:00
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My commit already had fastqc in there. And has been accepted. <3

My commit already had fastqc in there. And has been accepted. <3
J.v.N. closed this pull request 2021-02-15 17:07:50 +01:00

Pull request closed

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Reference: GRIAC/system_genetics#4
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