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Day1_answer_key.md

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Day 1 Answer Key

QC using FASTQC

  1. Once you have figured out what argument to use, run FastQC with 4 threads/cores.
$ fastqc -o ~/chipseq_workshop/results/fastqc/ -t 4 ~/chipseq_workshop/raw_data/wt*chip.fastq.gz
  1. Do you notice any difference in running time? Does multi-threading speed up the run?

Answer: Yes, multi-threading speeds up the run. Also, the progress bar on the screen shows that two samples are processed simultaneously, which is another indication of multi-threading.

Alignment using bowtie2

  1. After your job has completed, check the resulting .out and .err files. What information do you obtain from each file?

Answer: The .out file is empty. The .err file contains the alignment statistics.

  1. Take a quick peek at a sample BAM file using samtools view. Does the information you see line up with the fields we described above?
samtool view -h ~/chipseq_workshop/results/bowtie2/wt_sample2_chip.bam | less

Answer: Using the less command is helpful in allowing your to scroll through the file. You should see lines corresponding to each read and a short header section.

  1. What is the alignment rate for the wt_sample2_chip? Do you think the alignment is good?

Answer: The alignment rate is 98.34%. The alignment is good.