units example with peaks

README.md

 
 
-## Analysis Workflow
+## Analysis Workflow for Cut&Tag experiment
 
-A snakemake pipeline is available: https://github.com/maxsonBraunLab/cutTag-pipeline
+This Snakemake template is inspired from https://github.com/maxsonBraunLab/cutTag-pipeline
 
 
 It used a specific peak caller for Cut&Tag: [gopeaks](https://github.com/maxsonBraunLab/gopeaks) and published in [Genome Biol](https://doi.org/10.1186/s13059-022-02707-w)
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config/samples.tsv

 sample	condition
-WT_A	WT
-WT_B	WT
-KO_A	KO
-KO_C	KO
+TF_DAneuronD15	TF_DA15
+K27_DAneuronD15	K27_DA15
+K27_DAneuronD30	K27_DA30
+K27_DAneuronD30_2	K27_DA30

config/units.tsv

-sample	unit	fq1	fq2	strandedness
-WT_A	1	fastq/BY_A.fastq.gz		reverse
-WT_A	2	fastq/BY_A-2.fastq.gz		reverse
-WT_B	1	fastq/BY_B.fastq.gz		reverse
-KO_A	1	fastq/BY_Gis1_A.fastq.gz		reverse
-KO_C	1	fastq/BY_Gis1_C.fastq.gz		reverse
+sample	unit	fq1	fq2	peaks
+TF_DAneuronD15	1	fastq/20220214_ZFHX4_DAneuron_day15_EPIFU_SB_S41_R1_001.fastq.gz	fastq/20220214_ZFHX4_DAneuron_day15_EPIFU_SB_S41_R2_001.fastq.gz	narrow
+K27_DAneuronD15	1	fastq/20220310_H3K27ac_DAneuron_day15_EPIFU_SB_S43_R1_001.fastq.gz	fastq/20220310_H3K27ac_DAneuron_day15_EPIFU_SB_S43_R2_001.fastq.gz	broad
+K27_DAneuronD30	1	fastq/20220301_H3K27ac_DAneuron_day30_EPIFU_SB_S42_R1_001.fastq.gz	fastq/20220301_H3K27ac_DAneuron_day30_EPIFU_SB_S42_R2_001.fastq.gz	broad
+K27_DAneuronD30_2	1	fastq/20220323_H3K27ac_DAneuron_day30_EPIFU_SB_S44_R1_001.fastq.gz	fastq/20220323_H3K27ac_DAneuron_day30_EPIFU_SB_S44_R2_001.fastq.gz	broad