SansamLab/Cut_And_Run_Analysis_SnakeMake-v1.1.1.zip
SansamLab-Cut_And_Run_Analysis_SnakeMake-45e3628
.gitattributes
66 Bytes
InstructionsForHpcRun.md
692 Bytes
LICENSE
1.1 kB
README.md
21.4 kB
config
cluster_config_template.yml
2.7 kB
config_template.yml
1.8 kB
samples_template.csv
758 Bytes
graphic.png
245.7 kB
resources
Report.Rmd
2.4 kB
TruSeq3-PE-2.fa
260 Bytes
build_multi_genome
README.md
1.1 kB
build_hg38_ec_dm_multi_genome.sh
1.4 kB
build_hg38_ec_multi_genome.sh
955 Bytes
chromosome_sizes
README.md
256 Bytes
danRer10.chrom.sizes
24.0 kB
danRer11.chrom.sizes
48.1 kB
danRer7.chrom.sizes
18.7 kB
dm6.chrom.sizes
45.1 kB
hg19.chrom.sizes
2.0 kB
hg38.chrom.sizes
11.7 kB
mm10.chrom.sizes
1.4 kB
mm39.chrom.sizes
1.4 kB
mm9.chrom.sizes
584 Bytes
hg19-blacklist.v2.bed
34.9 kB
hg38-blacklist.v2.bed
26.9 kB
test_S7_R1_001_sub.fastq.gz
2.4 MB
test_S7_R1_001_sub_copy.fastq.gz
2.4 MB
test_S7_R2_001_sub.fastq.gz
2.5 MB
test_S7_R2_001_sub_copy.fastq.gz
2.5 MB
useful_scripts
make_md5_hashes.sh
902 Bytes
results
README
0 Bytes
logs
README
0 Bytes
workflow
Snakefile
21.1 kB
common_functions.py
2.9 kB
envs
CutAndRun_Conda_Environment.yml
8.4 kB
R_Report.yml
11.4 kB
SnakemakeEnv2.yml
7.9 kB
align_reads_with_bowtie2.yml
1.4 kB
callPeaks.yml
2.7 kB
deeptools.yml
2.5 kB
fastqc_reads.yml
2.4 kB
qc_trim_align.yml
17.1 kB
samtools.yml
810 Bytes
sicer2.yml
1.2 kB
trim_reads_with_cutadapt.yml
1.1 kB
trim_reads_with_trimmomatic.yml
2.3 kB
scripts
Make_final_report.R
328 Bytes