From da722539c7c90f77b2ed5b98c89d41360f7566d7 Mon Sep 17 00:00:00 2001 From: Aurelien Ginolhac <ginolhac@gmail.com> Date: Thu, 19 Jan 2023 16:38:52 +0100 Subject: [PATCH] units example with peaks --- README.md | 4 ++-- config/samples.tsv | 8 ++++---- config/units.tsv | 11 +++++------ 3 files changed, 11 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 9e55c0e..132779e 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ -## 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) \ No newline at end of file diff --git a/config/samples.tsv b/config/samples.tsv index f7021a0..370c36c 100644 --- a/config/samples.tsv +++ b/config/samples.tsv @@ -1,5 +1,5 @@ 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 diff --git a/config/units.tsv b/config/units.tsv index bb3706f..887588d 100644 --- a/config/units.tsv +++ b/config/units.tsv @@ -1,6 +1,5 @@ -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 -- GitLab