GRADING EXERCISE

Make a pipeline that does the following:

• Aligns reads in fastq files (there are two files from a ChIP-seq experiment) in the folder testdata using Bowtie (as in the course exercises) to the chr19 (file chr19.fasta.gz).

• Runs FastQC on the fastq files and the files produced in the result of the read alignment.

• Calls ChIP-seq peaks for the produced alignments using the MACS2 software (here is the official container).

(Optional) Make a more complex pipeline that does all the above plus:

• Allows optional (as a parameter) read alignment using Bowtie, Bowtie2 or BWA.

• Compares the number of called peaks for different alignment programs.

• Compares required computational resources and execution time for running the pipeline (all or/and only alignment) for different alignment programs.

Email your full solution (we should be able to run your pipeline) at BioinformaticsUnit@crg.eu or, better, do a pull request in this repository. Please use your First and Second name in the name of your folder.

Deadline: 28 November 2021 23:59