Bisulfite conversion WGBS
- Paul Whatmore (Deactivated)
- Roberto Barrero Gumiel
Test bisulfate conversion rate
See email from Vikki 12-02-2023.
Hi Roberto and Paul,
The Bisulfate test run has completed if you could still help with checking the conversion efficiency?
Here’s the links to BaseSpace:
Run:
Project:
Sample “test 1” should be the converted sample and the “test 2” should be the non-converted DNA.
Thank you and let me know if you have any questions.
Best wishes,
Vikki
Download data from Basespace.
Followed this guide: Downloading data from BaseSpace
PBS job submitted:
#!/bin/bash -l
#PBS -N fetchBaseSpace
#PBS -l walltime=24:00:00
#PBS -l mem=32gb
#PBS -l ncpus=8
#PBS -m bae
#PBS -M paul.whatmore@qut.edu.au
#PBS -j oe
cd $PBS_O_WORKDIR
#fetch data from BaseSpace by indicating the Project ID (-i parameter)
bs download project -i 382493133 -o /work/eresearch_bio/projects/CARF/Alison_Carey_WGBS/data --extension=fastq.gz
Raw data downloaded to /work/eresearch_bio/projects/CARF/Alison_Carey_WGBS/data
Initial data management
Fastq files moved to /work/eresearch_bio/projects/CARF/Alison_Carey_WGBS/fastq
mv /work/eresearch_bio/projects/CARF/Alison_Carey_WGBS/data/**/*.fastq.gz /work/eresearch_bio/projects/CARF/Alison_Carey_WGBS/fastqFiles are two paired-end samples: ‘test-1’ and ‘test-2’. These are across 8 files in the raw data. Each read pair spans a lane, so fastq files needs to be concatenated by lane.
Doing this via an interactive PBS session:
qsub -I -S /bin/bash -l walltime=11:59:00 -l select=1:ncpus=32:mem=128gbConcatenating lanes (run in fastq directory):
# Combining test 1 first read pairs
cat *test-1*R1_001.fastq.gz > test_1_R1.fastq.gz
# Combining test 1 second read pairs
cat *test-1*R2_001.fastq.gz > test_1_R2.fastq.gz
# Combining test 2 first read pairs
cat *test-2*R1_001.fastq.gz > test_2_R1.fastq.gz
# Combining test 2 second read pairs
cat *test-2*R2_001.fastq.gz > test_2_R2.fastq.gzThen can remove all the original datafiles rm Alison*