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download from SRA
October 2, 2016
After getting all the files, the first step of analysis will be to assess the quality of the reads generated.
FastQC is a good tool for this. I'll be generating reports for each lane separately to check for any lane bias. Also as these are paired end reads (PE) we will run a fastqc on each read file.
Eventually, these will all be concatenated to one file per sample.
Edit: After looking at the files again and at the email from our genomics core. The sequencing was performed on only one lane. My mistake.
1) Make a txt file with all the fastq files in the dir. This will allow for running a PBS array. Also make a dir for all the result files.
2) Sh script to run FastQC on all of the fastq files:
Some comments on this sh: the -noextract flag will keep the results in zip format. The -o flag will direct the output to the "FastQC/Original" dir.
30min was too short for these files I added 15min to the Required runtime.
For info on reading and interpretation of the FastQC results:
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