christacaggiano / circle_rna

Circle RNA exploration

Circle_RNA

The effects of editing sites were probed using the Variant Effect Predictor from ENSEMBL:

commands used to generate VEF input files - reference original perl scripts written by R. Rahman for the Rosbash Lab 2016 

perl editsites_to_basecall.pl base_call_input.txt > base_call_even.txt 

perl create_variant_predictor_input.pl -b base_call_even.txt -s UCSC_table_output_strandedness.txt > variant_predictor_output.txt

Introns flanking known circular RNA were found using UCSC table browser and bedtools:

---dm6 introns were generated using the table browser Assembly- dm6 Group- genes and gene predictions Track- refSeq Table- refGene Output- bed Create one bed ouput per- introns

---flanking regions were generated from known circular rna bed file

bedtools flank -i mmc_dm6_bed.txt -g genome.fa.fai -b 300 > flankOut.txt

---known introns were compared to flanking regions and reported using bedtools left outer join

bedtools intersect -a flankOut.txt -b dm6_introns_bed.txt -loj > intron_intersect.txt