Good Afternoon Emilie: I don't have the archive of the knownToEnsembl.txt file, however, I do have a copy of the genePred file for the ensGene track version60:
http://genome-test.cse.ucsc.edu/~hiram/ensGene.hg19.v60/hg19.ensGene.gp.gz The simple awk script included below can convert this genePred file to a bed file. --Hiram Emilie Chautard wrote: > Hi, > > I need to use the Ensembl r60 gene annotations for the files > knownToEnsembl.txt and ensGene.txt. > It seems that the files on > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ correspond to a > more recent release. > Do you have a tool to suggest which could help me to generate these files > or are these files still available somewhere? > Thanks a lot in advance, > Best regards, > > Emilie #!/usr/bin/awk -f # # Convert genePred file to a bed file (on stdout) # BEGIN { FS="\t"; OFS="\t"; } { name=$1 chrom=$2 strand=$3 start=$4 end=$5 cdsStart=$6 cdsEnd=$7 blkCnt=$8 delete starts split($9, starts, ","); delete ends split($10, ends, ","); blkStarts="" blkSizes="" for (i = 1; i <= blkCnt; i++) { blkSizes = blkSizes (ends[i]-starts[i]) ","; blkStarts = blkStarts (starts[i]-start) ","; } print chrom, start, end, name, 1000, strand, cdsStart, cdsEnd, 0, blkCnt, blkSizes, blkStarts } _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
