This branch contains test data to be used for automated testing with the nf-core/atacseq pipeline.
design.csv
: Experiment design file for minimal test dataset
design_full.csv
: Experiment design file for full test dataset
reference/
: Genome reference files (iGenomes R64-1-1 Ensembl release)
testdata/
: FastQ files sub-sampled to 100,000 paired-end reads
S. cerevisiae paired-end ATAC-seq dataset was obtained from:
Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ. Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. Genome Res 2015 Nov;25(11):1757-70. Pubmed GEO
GEO_ID | SRA_ID | SAMPLE_NAME |
---|---|---|
GSM1621339 | SRR1822153 | Osmotic Stress Time 0 A rep1 |
GSM1621340 | SRR1822154 | Osmotic Stress Time 0 A rep2 |
GSM1621343 | SRR1822157 | Osmotic Stress Time 15 C rep1 |
GSM1621344 | SRR1822158 | Osmotic Stress Time 15 C rep2 |
GSM1621345 | SRR1822159 | Osmotic Stress Time 30 D rep1 |
GSM1621346 | SRR1822160 | Osmotic Stress Time 30 D rep2 |
The example command below was used to sub-sample the raw paired-end FastQ files to 100,000 reads (see seqtk).
mkdir -p sample
seqtk sample -s100 SRR1822153_1.fastq.gz 100000 | gzip > ./sample/SRR1822153_1.fastq.gz
seqtk sample -s100 SRR1822153_2.fastq.gz 100000 | gzip > ./sample/SRR1822153_2.fastq.gz
To track and test the reproducibility of the pipeline with default parameters below are some of the expected outputs.
sample | peaks |
---|---|
OSMOTIC_STRESS_T0_R1 | 890 |
OSMOTIC_STRESS_T0_R2 | 627 |
OSMOTIC_STRESS_T15_R1 | 1133 |
OSMOTIC_STRESS_T15_R2 | 1135 |
sample | peaks |
---|---|
OSMOTIC_STRESS_T0 | 1130 |
OSMOTIC_STRESS_T15 | 1395 |
These are just guidelines and will change with the use of different software, and with any restructuring of the pipeline away from the current defaults.
H. sapiens paired-end ATAC-seq dataset was obtained from:
M Ryan Corces et al. An Improved ATAC-seq Protocol Reduces Background and Enables Interrogation of Frozen Tissues. Nat Methods. 2017 Oct;14(10):959-962. doi: 10.1038/nmeth.4396. Pubmed SRA
SRA ID | SAMPLE NAME |
---|---|
SRR5427884 | ATAC-seq of in vitro culture GM12878 using the Standard ATAC method |
SRR5427885 | ATAC-seq of in vitro culture GM12878 using the Standard ATAC method |
SRR5427886 | ATAC-seq of in vitro culture GM12878 using the Omni-ATAC method |
SRR5427887 | ATAC-seq of in vitro culture GM12878 using the Omni-ATAC method |
SRR5427888 | ATAC-seq of in vitro culture GM12878 using the Fast-ATAC method |
SRR5427889 | ATAC-seq of in vitro culture GM12878 using the Fast-ATAC method |