06_seminar.md

Seminar 6 Coding Material

nf-core/atacseq

Basic run command

nextflow run nf-core/atacseq \
    --input samplesheet.csv \
    --outdir <OUTDIR> r \
    --genome GRCh37 \
    --read_length <50> \
    -profile <docker> \
    -r <2.1.1>

--input

Samplesheet (.csv)

Biological Replicates

sample,fastq_1,fastq_2,replicate
CONTROL,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,1
CONTROL,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,2
CONTROL,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,3

Technical replicates

sample,fastq_1,fastq_2,replicate
CONTROL,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,1
CONTROL,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,1
CONTROL,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,1

Controls for peak calling

sample,fastq_1,fastq_2,replicate,control,control_replicate
CONTROL,AEG588A1_S1_L002_R1_001.fastq.gz,,1,,
CONTROL,AEG588A2_S2_L002_R1_001.fastq.gz,,2,,
CONTROL,AEG588A3_S3_L002_R1_001.fastq.gz,,3,,
TREATMENT,AEG588A4_S4_L003_R1_001.fastq.gz,,1,CONTROL,1
TREATMENT,AEG588A5_S5_L003_R1_001.fastq.gz,,2,CONTROL,2
TREATMENT,AEG588A6_S6_L003_R1_001.fastq.gz,,3,CONTROL,3