NGS-Var2020 Exercise.1
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QC paired end reads using fastQC
You should have learned how to use FastQC during the Introductory training session. We now apply it to the sample data for the sake of time and to build this as a reflex in your Trainee's mind.
Apply FastQC to the FastQ data
You usually receive FastQ data from your sequence provider. It is always good to inspect it prior to starting analyses as it may be biased by artefacts and 'may' in that case need cleaning.
We could also use the fastQC GUI version to do this and will return to GenePattern after that
Q: What if you got a unique fastq file containing interleaved paired reads?
You can ignore this fact and run FastQC on the interleaved data but generally reverse reads of the pair are less pretty than forward reads and you will get the mixture of both in the QC plots. Otherwise, you can easily convert the unique fastQ file to two files, one for each read of a pair by using a number of tools found on the web then run fastQC twice. We recommend a simple bash tool developed by Nathan S. Watson-Haigh that will do the job very fast and can be found HERE. Just copy paste the code to a script under unix terminal then give it your fastq as input.
review fastQC results
The FastQC tool stores all results in a html file and linked pictures. You can review these results after decompressing the zip files created above. The QC results for the first read in pair data (10% sample) ares used to exemplify this.
You should get something like this (read1, read2).
Have a look at https://sequencing.qcfail.com/software/fastqc/ to find examples of QC failures
download exercise files
Download exercise files here
References:
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