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Versions of Tools and Reference Files Used in Chips

Tools

environment: chips(stable)

Software Version Source Notes
snakemake 5.4.5 bioconda
samtools 1.10 bioconda
python 3.6.12 conda-forge
r 3.5.1 conda-forge
numpy 1.17.3 conda
bwa 0.7.15 bioconda
bowtie2 2.3.4.1 bioconda
picard 2.20.0 bioconda
bedtools 2.27.1 bioconda
seqtk 1.3 bioconda
fastqc 0.11.9 bioconda
fastp 0.20.1 bioconda
ggplot2 3.3.0 conda-forge r
reshape2 1.4.4 conda-forge r
git 2.26.0 conda-forge
perl 5.26.2 conda-forge
homer 4.11 bioconda
weblogo 2.8.2 bioconda
seqLogo 1.50.0 bioconda bioconductor
bedgraphtobigwig 377 bioconda ucsc
bedsort 377 bioconda ucsc
qdnaseq 1.18.0 bioconda bioconductor
seaborn 0.11.1 conda-forge
r.utils 2.9.2 conda-forge r
pybigwig 0.3.17 bioconda
pybedtools 0.8.1 bioconda
numpy 1.19.5 conda
cython 0.29.21 conda
jinja2 2.11.2 conda
macs2 2.2.7.1 bioconda

Reference

All reference file could be downloaded from here.

CIDC

GDC_hg38
Reference Key Location Version Source Notes
bwa_index ./ref_files/GDC_hg38/bwa_indices/GRCh38.d1.vd1.fa GRCh38 https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files GDC.h38.d1.vd1 BWA Index Files
geneTable ./ref_files/GDC_hg38/GDC_hg38.refGene GENCODE v22 Download from UCSC genome table browser used for calculate ceas and CNV
geneBed ./ref_files/hg38/GDC_hg38.bed GENCODE v22 reformat gtf by CHIPS/static/scripts/GtfToBed.py used for calculating RP
conservation ./ref_files/GDC_hg38/conservation/ GRCh38, 100way https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons100way/
DHS ./ref_files/GDC_hg38/regions/hg38_cCREs.bed cCRE regions from ENCODE Project
exons ./ref_files/GDC_hg38/regions/exon.bed GENCODE v22 extract from geneTable
promoters ./ref_files/GDC_hg38/regions/promoter.bed GENCODE v22 extract from geneTable
velcro_regions MISSING - - Blacklist Region
chrom_lens ./ref_files/GDC_hg38/regions/chromInfo_hg38.txt extract from rawgenome by samtools faidx
rawgenome (not in ref.yaml) ./ref_files/GDC_hg38/rawgenome split rawgenome into each chromosome required by MDSeqPos
masked (not in ref.yaml) ./ref_files/GDC_hg38/masked required by MDSeqPos

Cistrome

hg38
Reference Key Location Version Source MD5 Notes
bwa_index ./ref_files/hg38/bwa_indices/hg38/hg38.fa hg38 http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromFa.tar.gz use bwa to build index
geneTable ./ref_files/hg38/hg38.refGene refseq hg38 refseq from UCSC table browser Calculate RP
geneBed ./ref_files/hg38/hg38_refGene.bed refseq hg38 reformat feature table by CHIPS/static/scripts/FeatureTableToBed.py
conservation ./ref_files/hg38/conservation/hg38.phastCons100way.bw hg38, 100way https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons100way/ Previous using 7way in Cistrome DB
DHS ./ref_files/hg38/regions/DHS_hg38.bed Union DHS regions from Cistrome DB
exons ./ref_files/hg38/regions/exon.bed extract from geneTable
promoters ./ref_files/hg38/regions/promoter.bed extract from geneTable
velcro_regions MISSING - - Blacklist Region
chrom_lens ./ref_files/hg38/regions/chromInfo_hg38.txt UCSC table browser
rawgenome ./ref_files/hg38/rawgenome/ http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromFa.tar.gz required by MDSeqPos
masked ./ref_files/hg38/masked/ http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromFaMasked.tar.gz required by MDSeqPos
mm10
Reference Key Location Version Source MD5 Notes
bwa_index ./ref_files/mm10/bwa_indices/mm10.fa mm10 http://hgdownload.cse.ucsc.edu/goldenpath/mm10/bigZips/chromFa.tar.gz use bwa to build index
geneTable ./ref_files/mm10/mm10.refGene refseq mm10 refseq from UCSC table browser Calculate RP
geneBed ./ref_files/mm10/mm10_refGene.be refseq mm10 reformat feature table by CHIPS/static/scripts/FeatureTableToBed.py
conservation ./ref_files/mm10/conservation/mm10.60way.phastCons.bw mm10, 60way Previous using 60way in Cistrome DB
DHS ./ref_files/mm10/regions/mm10.DHS.bed Union DHS regions from Cistrome DB merging all the peaks of DNase-seq data from ENCODE
exons ./ref_files/mm10/regions/mm10.exon.bed extract from geneTable
promoters ./ref_files/mm10/regions/mm10.promoter.bed extract from geneTable
velcro_regions MISSING - - Blacklist Region
chrom_lens ./ref_files/mm10/regions/mm10.len UCSC table browser
rawgenome ./ref_files/hg38/rawgenome/ http://hgdownload.cse.ucsc.edu/goldenpath/mm10/bigZips/chromFa.tar.gz required by MDSeqPos
masked ./ref_files/hg38/masked/ http://hgdownload.cse.ucsc.edu/goldenpath/mm10/bigZips/chromFaMasked.tar.gz required by MDSeqPos

Contamination Panel

Reference Key Location Version Source MD5 Notes
hg19 ./ref_files/contam_panel/hg19/hg19.fa
mm9 ./ref_files/contam_panel/mm9/mm9.fa
dm3 ./ref_files/contam_panel/dm3/dm3.fa
S_cerevisiae ./ref_files/contam_panel/S_cerevisiae/S_cerevisiae.fa
e_coli ./ref_files/contam_panel/e_coli/e_coli.fasta
myco_PG-8A ./ref_files/contam_panel/mycoplasma/GCF_000018785.1_ASM1878v1/myco_PG-8A.fna
myco_ATCC23114 ./ref_files/contam_panel/mycoplasma/GCF_000085865.1_ASM8586v1/myco_ATCC23114.fna
myco_m64 ./ref_files/contam_panel/mycoplasma/GCF_000186005.1_ASM18600v1/myco_m64.fna
myco_SK76 ./ref_files/contam_panel/mycoplasma/GCF_000313635.1_ASM31363v1/myco_SK76.fna
myco_ATCC23714 ./ref_files/contam_panel/mycoplasma/GCF_000420105.1_ASM42010v1/myco_ATCC23714.fna
myco_ATCC23064 ./ref_files/contam_panel/mycoplasma/GCF_000485555.1_ASM48555v1/myco_ATCC23064.fna
myco_HAZ145_1 ./ref_files/contam_panel/mycoplasma/GCF_001547975.1_ASM154797v1/myco_HAZ145_1.fna
myco_ATCC29342 ./ref_files/contam_panel/mycoplasma/GCF_000027345.1_ASM2734v1/myco_ATCC29342.fna
myco_R ./ref_files/contam_panel/mycoplasma/GCF_000092585.1_ASM9258v1/myco_R.fna
myco_WVU1853 ./ref_files/contam_panel/mycoplasma/GCF_000969765.1_ASM96976v1/myco_WVU1853.fna