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Code Block
languagebash
titleRunning FastQC example
collapsetrue
mkdir $SCRATCH/GVA_fastqc_tutorial
cd $SCRATCH/GVA_fastqc_tutorial
cp $BI/gva_course/mapping/data/SRR030257_1.fastq .
 
fastqc -h  # examine program options
fastqc SRR030257_1.fastq  # run the program


Note
titlePotential error with fastqc program execution

As noted during Monday's class, several people were experiencing an that included text:


No Format
Can't locate warnings.pm:   /corral-repl/utexas/BioITeam//local/share/perl5/warnings.pm: Permission denied at /home1/08965/vramirez/miniconda3/envs/fastqc-test/bin/fastqc line 2.
BEGIN failed--compilation aborted at /home1/08965/vramirez/miniconda3/envs/fastqc-test/bin/fastqc line 2.

This is believed to be related to the occasional "permission is denied" error some were getting when trying to access the BioITeam contents. If you have circled back to this, and are experiencing this error please get my attention. I have been unable to troubleshoot this fully as I have not been having the problem, but I believe the answer will be found in:

Code Block
languagebash
titlecommands for troubleshooting fastqc error
perl -V  #bottom @INC: section
perldoc -l warnings  # should list the specific version of the warnings module attempted to be being used
echo $PERL5LIB

Solution will likely be modifying $PERL5LIB away from BioITeam contents which should force conda environment versions.



Expand
titleWhat results did you get from your FastQC analysis?


No Format
titlels -l shows something like this
-rwxr-xr-x 1 ded G-802740 498588268 Jun 13 12:06 SRR030257_1.fastq
-rw-r--r-- 1 ded G-802740    291714 Jun 13 12:07 SRR030257_1_fastqc.html
-rw-r--r-- 1 ded G-802740    455677 Jun 13 12:07 SRR030257_1_fastqc.zip

The SRR030257_1.fastq file is what we analyzed, so FastQC created the other two items. SRR030257_1_fastqc.html represents the results in a file viewable in a web browser. SRR030257_1_fastqc.zip is just a Zipped (compressed) version of the results.

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