8. Appendix

8.1. Correspondence table for the genome build

While download_genomedata.sh uses the Ensembl genome build, Churros uses UCSC genome build in the command. Here we summarize the correspondence.

Species	Ensembl	UCSC
human	GRCh38	hg38
human	GRCh37	hg19
mouse	GRCm39	mm39
mouse	GRCm38	mm10
rat	mRatBN7.2	rn7
fly	BDGP6	dm6
zebrafish	GRCz11	danRer11
chicken	GRCg6a	galGal6
C.elegans	WBcel235	ce11
S.serevisiae	R64-1-1	sacCer3
African clawed frog	Xenopus_tropicalis	xenLae2

For example, to use human genome build GRCh38/hg38, specify GRCh38 or hg38 for download_genomedata.sh and hg38 for churros.

download_genomedata.sh hg38 UCSC-hg38/ 2>&1 | tee log/UCSC-hg38
churros -p 24 --mpbl samplelist.txt samplepairlist.txt hg38 UCSC-hg38
# or
download_genomedata.sh GRCh38 Ensembl-GRCh38/ 2>&1 | tee log/Ensembl-GRCh38
churros -p 24 --mpbl samplelist.txt samplepairlist.txt hg38 Ensembl-GRCh38/

Other species:

Species	ID
human	T2T
S.pombe	SPombe
A.thaliana	TAIR10
Oryzias latipes	Medaka
Hydra vulgaris AEP	HVAEP

8.2. Make mappability files

If you want to make the mappability files by yourself, you can use calculate_mappability_mosaics.sh.

calculate_mappability_mosaics.sh [Options] <Ddir>
   <Ddir>: directory of the genome
   Options:
      -f <int>: fragment length (default: 150)
      -b <array <int>>: binsizes (default: "10000 25000 50000 500000 1000000")
      -r <array <int>>: read length (default: "36 50")
      -p <int>: number of CPUs (default: 12)
   Example:
      calculate_mappability_mosaics.sh Ensembl-GRCh38

For example, if you want to make the mappability files for genome build hg38 with the read length 75 and 100, type:

calculate_mappability_mosaics.sh -r "75 100" UCSC-hg38

Then the data is created in UCSC-hg38/mappability_Mosaics_75mer and UCSC-hg38/mappability_Mosaics_100mer.

Note

This command takes long time for computation. Set large number for -p (e.g., 64).