Commit 45d9a3a5 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Add only transcript ids.

parent ce840017
This diff is collapsed.
This source diff could not be displayed because it is too large. You can view the blob instead.
This diff is collapsed.
This diff is collapsed.
......@@ -6,10 +6,10 @@ awk '{if($20=="\"snoRNA\";"){print $0}}' gencode.v19.annotation.gtf > gencode.v1
# Make a index to map gene_id to gene_names
grep transcript gencode.v19.annotation_protein_coding.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > gencode.v19.annotation_protein_coding_mapping.txt
grep transcript gencode.v19.annotation_lncRNA.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > gencode.v19.annotation_lncRNA_mapping.txt
grep transcript gencode.v19.annotation_snRNA.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > gencode.v19.annotation_snRNA_mapping.txt
grep transcript gencode.v19.annotation_snoRNA.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > gencode.v19.annotation_snoRNA_mapping.txt
grep transcript gencode.v19.annotation_protein_coding.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' | grep ENST > gencode.v19.annotation_protein_coding_mapping.txt
grep transcript gencode.v19.annotation_lncRNA.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' | grep ENST > gencode.v19.annotation_lncRNA_mapping.txt
grep transcript gencode.v19.annotation_snRNA.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' | grep ENST > gencode.v19.annotation_snRNA_mapping.txt
grep transcript gencode.v19.annotation_snoRNA.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' | grep ENST > gencode.v19.annotation_snoRNA_mapping.txt
grep transcript gencode.v19.annotation.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' > mapping.txt
grep transcript gencode.v19.annotation.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g'| grep ENST > mapping.txt
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment