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drpatelh merged 6 commits into from
Mar 26, 2020
Merged

Add full test-dataset #136

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Add full design
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26 changes: 22 additions & 4 deletions README.md
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Expand Up @@ -4,11 +4,12 @@ This branch contains test data to be used for automated testing with the [nf-cor

## Content of this repository

`design.csv`: Experiment design file
`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

## Dataset origin
## Minimal test dataset origin

*S. cerevisiae* paired-end ATAC-seq dataset was obtained from:

Expand All @@ -23,7 +24,7 @@ Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ. Structu
| GSM1621343 | SRR1822157 | Osmotic Stress Time 15 C rep1 |
| GSM1621344 | SRR1822158 | Osmotic Stress Time 15 C rep2 |

## Sampling procedure
### Sampling procedure

The example command below was used to sub-sample the raw paired-end FastQ files to 100,000 reads (see [seqtk](https://github.com/lh3/seqtk)).

Expand All @@ -33,7 +34,7 @@ seqtk sample -s100 SRR1822153_1.fastq.gz 100000 | gzip > ./sample/SRR1822153_1.f
seqtk sample -s100 SRR1822153_2.fastq.gz 100000 | gzip > ./sample/SRR1822153_2.fastq.gz
```

## Expected output
### Expected output

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

Expand All @@ -54,3 +55,20 @@ To track and test the reproducibility of the pipeline with default parameters be
| 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:

Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013 Dec;10(12):1213-8. [Pubmed](https://www.ncbi.nlm.nih.gov/pubmed/24097267) [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47753)

### Sample information

| GEO_ID | SRA_ID | SAMPLE_NAME |
|-------------|-------------|------------------------|
| GSM1155964 | SRR891275 | CD4+_ATACseq_Day1_Rep1 |
| GSM1155965 | SRR891276 | CD4+_ATACseq_Day1_Rep2 |
| GSM1155966 | SRR891277 | CD4+_ATACseq_Day2_Rep1 |
| GSM1155967 | SRR891278 | CD4+_ATACseq_Day2_Rep2 |
| GSM1155968 | SRR891279 | CD4+_ATACseq_Day3_Rep1 |
| GSM1155969 | SRR891280 | CD4+_ATACseq_Day3_Rep2 |
7 changes: 7 additions & 0 deletions design_full.csv
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group,replicate,fastq_1,fastq_2
CD4_DAY1,1,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR891/SRR891275/SRR891275_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR891/SRR891275/SRR891275_2.fastq.gz
CD4_DAY1,2,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR891/SRR891276/SRR891276_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR891/SRR891276/SRR891276_2.fastq.gz
CD4_DAY2,1,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR891/SRR891277/SRR891277_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR891/SRR891277/SRR891277_2.fastq.gz
CD4_DAY2,2,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR891/SRR891278/SRR891278_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR891/SRR891278/SRR891278_2.fastq.gz
CD4_DAY3,1,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR891/SRR891279/SRR891279_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR891/SRR891279/SRR891279_2.fastq.gz
CD4_DAY3,2,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR891/SRR891280/SRR891280_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR891/SRR891280/SRR891280_2.fastq.gz