WGBS Test Data¶
Test Data¶
Dataset¶
| Stable ID | SRR892982 |
| Citation | Sun et al 2014 |
Genome¶
| Assembly | GRChm8, chr19 |
| Chromosome | 19 |
| Start | 3000000 |
| End | 4020000 |
Method¶
The full dataset was downloaded from ENA aligned to the genome using GEM.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR892/SRR892982/SRR892982_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR892/SRR892982/SRR892982_2.fastq.gz
gunzip SRR892982_1.fastq.gz
gunzip SRR892982_2.fastq.gz
wget "http://www.ebi.ac.uk/ena/data/view/CM001012&display=fasta&download=fasta&filename=entry.fasta" -O mouse.GRCm38.19.fasta
sed -n 40022200,41046060p GCA_000001635.6.fasta > mouse.GRCm38.19.fasta
bowtie2-build mouse.GRCm38.19.fasta mouse.GRCm38.19.idx
bowtie2 -x genome/mouse.GRCm38.19.idx -U data/SRR892982_1.fastq > SRR892982_1.sam
samtools view -h -o SRR892982_1.sam SRR892982_1.bam
awk 'BEGIN { FS = "[[:space:]]+" } ; $3 ~ /CM001012/ {print $1}' SRR892982_1.sam > SRR892982_1.chr19.rows
python scripts/ExtractRowsFromFASTQs.py --input_1 tests/data/SRR892982_1.fastq --input_2 tests/data/SRR892982_2.fastq --rows SRR892982_1.chr19.rows --output_tag profile
mv data/tmp/SRR892982_1.profile_0.fastq data/SRR892982_1.chr19.fastq
mv data/tmp/SRR892982_2.profile_0.fastq data/SRR892982_2.chr19.fastq
bowtie2 -x genome/mouse.GRCm38.19.idx -1 data/SRR892982_1.chr19.fastq -2 data/SRR892982_2.chr19.fastq > SRR892982_1.chr19.sam
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There are a range of positive and negative peaks between 3000000 and 4020000. Subselect the genome and matching FASTQ reads for the required subsection:
1 2 3 4 5 6 7 8 9 10 11 | head -n 1 mouse.GRCm38.19.fasta > 3M/mouse.GRCm38.19.3M.fasta
sed -n 50001,67001p mouse.GRCm38.19.fasta >> 3M/mouse.GRCm38.19.3M.fasta
bowtie2-build 3M/mouse.GRCm38.19.3M.fasta 3M/mouse.GRCm38.19.3M.idx
bowtie2 -p 4 -x 3M/mouse.GRCm38.19.3M.idx -1 SRR892982_1.chr19.fastq -2 SRR892982_2.chr19.fastq > 3M/SRR892982.chr19.3M.sam
samtools view -h -o 3M/SRR892982.chr19.3M.sam 3M/SRR892982.chr19.3M.bam
python scripts/ExtractRowsFromFASTQs.py --input_1 SRR892982_1.chr19.fastq --input_2 SRR892982_2.chr19.fastq --rows 3M/SRR892982.chr19.3M.rows --output_tag subset
mv tmp/SRR892982_1.chr19.subset_0.fastq 3M/SRR892982_1.chr19.3M.fastq
mv tmp/SRR892982_2.chr19.subset_0.fastq 3M/SRR892982_2.chr19.3M.fastq
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This has enough load to test the system, while also generating results in the output files.
These files are then saved in the tests/data directory as:
1 2 3 | bsSeeker.Mouse.GRCm38.fasta
bsSeeker.Mouse.SRR892982_1.fastq.gz
bsSeeker.Mouse.SRR892982_2.fastq.gz
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These files were too large for use within the Travis tst environment, so the number of entries was reduced by taking every other read:
1 2 3 4 5 6 7 8 | sed -n -e '0~9{N;N;N;N;p}' tests/data/bsSeeker.Mouse.SRR892982_1.fastq > tests/data/test_bsSeeker.Mouse.SRR892982_1.fastq
sed -n -e '0~9{N;N;N;N;p}' tests/data/bsSeeker.Mouse.SRR892982_2.fastq > tests/data/test_bsSeeker.Mouse.SRR892982_2.fastq
mv tests/data/test_bsSeeker.Mouse.SRR892982_1.fastq tests/data/bsSeeker.Mouse.SRR892982_1.fastq
mv tests/data/test_bsSeeker.Mouse.SRR892982_2.fastq tests/data/bsSeeker.Mouse.SRR892982_2.fastq
gzip tests/data/bsSeeker.Mouse.SRR892982_1.fastq
gzip tests/data/bsSeeker.Mouse.SRR892982_2.fastq
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Test Scripts¶
The following are the tests for checking that the tools in the WGBS pipeline are functioning correctly.
The tests should be run in this order so that the required input files are generated at the correct stage.
1 2 3 4 5 | pytest -m wgbs tests/test_fastqc_validation.py
pytest -m wgbs tests/test_bs_seeker_filter.py
pytest -m wgbs tests/test_bs_seeker_indexer.py
pytest -m wgbs tests/test_bs_seeker_aligner.py
pytest -m wgbs tests/test_bs_seeker_methylation_caller.py
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These can be called as part of a single tool chain with:
1 | python tests/test_toolchains.py --pipeline wgbs
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