Ctrl+K

Appendix

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

human

T2T

T2T

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

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/

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).

Contents