I downloaded the Nov. 2020 (mRatBN7.2/rn7) assembly of the rat genome (rn7) 2bit file from https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/
I pulled the rat info from gene2accession file using NCBI txid 10116
gunzip -c gene2accession.gz | grep '^10116\t' > ~/Desktop/jiraIssues/3362/10116.gene2accession.txt
I created bed 14 files for UCSC refGene and NCBI Ref Seq (ncbiRefSeq):
ucscToBedDetail.py -a 10116.gene2accession.txt -g Rattus_norvegicus.gene_info R_norvegicus_Nov_2020_refGene.bed.gz R_norvegicus_Nov_2020_refGene.bed
ucscToBedDetail.py -a 10116.gene2accession.txt -g Rattus_norvegicus.gene_info R_norvegicus_Nov_2020_ncbiRefSeq.bed.gz R_norvegicus_Nov_2020_ncbiRefSeq.bed
I then sorted, bgzipped, and tabix indexed the two bed files:
sort -k1,1 -k2,2n R_norvegicus_Nov_2020_refGene.bed | bgzip > R_norvegicus_Nov_2020_refGene.bed.gz
tabix -0 -s 1 -b 2 -e 3 R_norvegicus_Nov_2020_refGene.bed.gz
sort -k1,1 -k2,2n R_norvegicus_Nov_2020_ncbiRefSeq.bed | bgzip > R_norvegicus_Nov_2020_ncbiRefSeq.bed.gz
tabix -0 -s 1 -b 2 -e 3 R_norvegicus_Nov_2020_ncbiRefSeq.bed.gz
Next I sorted, bgzipped, and tabix indexed the psl files for all_est and all_mrna:
gunzip \-c R_norvegicus_Nov_2020_all_est.psl.gz | grep -v bin | cut -f2- > R_norvegicus_Nov_2020_all_est.psl
sort -k14,14 -k16,16n R_norvegicus_Nov_2020_all_est.psl > sorted.psl
mv sorted.psl R_norvegicus_Nov_2020_all_est.psl
bgzip R_norvegicus_Nov_2020_all_est.psl
tabix -s 14 -b 16 -0 R_norvegicus_Nov_2020_all_est.psl.gz
gunzip \-c R_norvegicus_Nov_2020_all_mrna.psl.gz | grep -v bin | cut -f2- > R_norvegicus_Nov_2020_all_mrna.psl
sort -k14,14 -k16,16n R_norvegicus_Nov_2020_all_mrna.psl > sorted.psl
mv sorted.psl R_norvegicus_Nov_2020_all_mrna.psl
bgzip R_norvegicus_Nov_2020_all_mrna.psl
tabix -s 14 -b 16 -0 R_norvegicus_Nov_2020_all_mrna.psl.gz
I downloaded the Nov. 2020 (mRatBN7.2/rn7) assembly of the rat genome (rn7) 2bit file from https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/
I pulled the rat info from gene2accession file using NCBI txid 10116
I created bed 14 files for UCSC refGene and NCBI Ref Seq (ncbiRefSeq):
I then sorted, bgzipped, and tabix indexed the two bed files:
Next I sorted, bgzipped, and tabix indexed the psl files for all_est and all_mrna: