test-datasets: atacseq

This branch contains test data to be used for automated testing with the nf-core/atacseq pipeline.

Content of this repository

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

Minimal test dataset origin

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

Sample information

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

Sampling procedure

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

Expected output

To track and test the reproducibility of the pipeline with default parameters below are some of the expected outputs.

Number of mergedLibrary broadPeaks

sample	peaks
OSMOTIC_STRESS_T0_R1	890
OSMOTIC_STRESS_T0_R2	627
OSMOTIC_STRESS_T15_R1	1133
OSMOTIC_STRESS_T15_R2	1135

Number of mergedReplicate broadPeaks

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.

Full test dataset origin

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

Sample information

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