Lesson 11 Practice

In this session, participants will practice making bigWig files from the HBR-UHR alignment results.

As always, be sure to be signed on to Biowulf for this set of exercises.

Solution

ssh user@biowulf.nih.gov

Change into the /data/user/hbr_uhr_b4b folder.

Solution

cd `/data/user/hbr_uhr_b4b`

If not done already, request an interactive session with 12gb of RAM and 10gb of local temporary storage space.

Solution

sinteractive --mem=12gb --gres=lscratch:10

Load bedtools.

Solution

module load bedtools

Create bedGraph files from the HBR-UHR alignment results. Stay in /data/user/hbr_uhr_b4b and recall that these are RNA sequencing data. Write the bedGraph files to the folder hbr_uhr_hisat2.

Solution

cat hbr_uhr_samples.txt | parallel "bedtools genomecov -ibam hbr_uhr_hisat2/{}.bam -split -bg > hbr_uhr_hisat2/{}_hisat2.bg"

Next, index the chromosome 22 reference genome stored in the folder references with file name 22.fa. Which module is needed?

Solution

module load samtools

samtools faidx references/22.fa

Create bigWig files from the HBR-UHR bedGraph files. Which module needs to be loaded to do this? Stay in /data/user/hbr_uhr_b4b for this exercise.

Solution

module load ucsc

cat hbr_uhr_samples.txt | parallel "bedGraphToBigWig hbr_uhr_hisat2/{}_hisat2.bg references/22.fa.fai hbr_uhr_hisat2/{}_hisat2.bw"