HTseq 2019 Module 6 Lab Supplement

Informatics for High-throughput Sequencing Data Analysis 2019 Module 6 Lab Supplement

Generating a preqc report for the E. coli data set

# First build an FM-index of the two E. coli Illumina data sets:
sga index -t 4 -a ropebwt ecoli.illumina.15x.fastq
sga index -t 4 -a ropebwt ecoli.illumina.50x.fastq

# Next, we can run `sga preqc` to run the calculations and generate the PDF report.
sga preqc -t 4 ecoli.illumina.15x.fastq > ecoli.illumina.15x.preqc
sga preqc -t 4 ecoli.illumina.50x.fastq > ecoli.illumina.50x.preqc
python sga-preqc-report.py ecoli.illumina.15x.preqc ecoli.illumina.50x.preqc