Step 5.
Use the fetchChromSizes script from the
same directory to create a
chrom.sizes file for the UCSC database with which you are working (e.g., hg38).
Alternatively, you can download the
chrom.sizes file for any assembly hosted at UCSC from our
downloads page (click on "Full
data set" for any assembly). For example, the hg38.chrom.sizes file for the hg38
database is located at
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.
mafToBigMaf hg38 chr22_KI270731v1_random.maf stdout | sort -k1,1 -k2,2n > bigMaf.txt
bedToBigBed -type=bed3+1 -as=bigMaf.as -tab bigMaf.txt hg38.chrom.sizes bigMaf.bb Note that the hg38 in the mafToBigMaf hg38 command indicates the referenceDb and matches the +expected prefix of the primary species' sequence name, for instance hg38 for the +hg38.chr22_KI270731v1_random found in the input example chr22_KI270731v1_random.maf file.
Step 6. Follow the below steps to create the binary indexed mafFrames and mafSummary files to accompany your bigMaf file:
genePredSingleCover chr22_KI270731v1_random.gp single.gp
genePredToMafFrames hg38 chr22_KI270731v1_random.maf bigMafFrames.txt hg38 single.gp
bedToBigBed -type=bed3+8 -as=mafFrames.as -tab bigMafFrames.txt hg38.chrom.sizes bigMafFrames.bb
hgLoadMafSummary -minSeqSize=1 -test hg38 bigMafSummary chr22_KI270731v1_random.maf
cut -f2- bigMafSummary.tab | sort -k1,1 -k2,2n > bigMafSummary.bed
bedToBigBed -type=bed3+4 -as=mafSummary.as -tab bigMafSummary.bed hg38.chrom.sizes bigMafSummary.bb Step 7. Move the newly created bigMaf file (bigMaf.bb) to a web-accessible http, https or ftp location. If you generated the bigMafSummary.bb and/or bigMafFrames.bb files,