Commit 35c417bb authored by Venkat Malladi's avatar Venkat Malladi

Analysis of basal cell state

parent 721d6ff4
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......@@ -13,3 +13,16 @@ grep transcript gencode.v19.annotation_snoRNA.gtf | cut -f9 | cut -f1,2,5,8 -d
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
# Filter for Transcripts that also play host to ncRNA
bedtools intersect -wa -a gencode.v19.annotation_protein_coding.gtf -b gencode.v19.annotation_snRNA.gtf gencode.v19.annotation_snoRNA.gtf > ncRNA_overlap.gtf
grep transcript ncRNA_overlap.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_ncRNA_host.txt
bedtools intersect -wa -a gencode.v19.annotation_lncRNA.gtf -b gencode.v19.annotation_snRNA.gtf gencode.v19.annotation_snoRNA.gtf > ncRNA_overlap.gtf
grep transcript ncRNA_overlap.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_ncRNA_host.txt
# Make bed file format
gtf2bed < gencode.v19.annotation.gtf > gencode.v19.bed
grep -v exon gencode.v19.bed | grep ENST | awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"(substr($13, index($10,'transcript_id')))}' | sed 's/"//g' | sed 's/;//g' > gencode.v19.transcripts.bed
awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"(substr($0, index($0,$10)))}'
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