how to get circRNA fasta sequence from CIRI bed
hello everyone, i use the CIRI to get the bed file of circRNA.
But how can i get the circRNA sequence?
I try to use find_circ,but could only get the spliced reads.
what should i do?
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Kevin Blighe
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fanyucai1 •
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BEDTools getfasta
You can use BEDTools getFasta:
cat test.bed
5 1000000 1000500
9 5000 6000
bedtools getfasta -fi 1000Genomes/human_g1k_v37.fasta -bed test.bed -fo test.fasta
cat test.fasta
>5:1000000-1000500
GTTTTAACTAAACTAACTCCCCAAAAACTGGACACGTGACTTCACGAGGCTTTTGCCGAGGAGCCCTGGGCTGCAGGGAACATTAATGGGGTAGGTGCACCCAGGCAAGGATGTGGGCAGACCCTCCAGCCTCTTGTGGTCTGGGTGTGCCTTGGGAAATGGCCAGCAGGATTCTTCTTGGAGGCAAGCTGGAGATTTTTAGGTCCTGGGTTAGAGGGAGAACTATGCGATTCCTCTGAGAGACCTGGGGATGGAGGGACTGGACCCTTCCAGCCACCTGTGCTGAGCCCATCTGCTGCCTCCTAAGGGGCTCCTAAGGGGCAATGGGTGGAAGTCTCCTGGGCTATGCCCTGAGCAGACACCATCCTTTTTGCTCCTTGGCAAAGATGCCTCTCAGGATCAAAGACCTGGTGGCCTGGTCCCTCCAGGAGGAATGGGAGGGCCAGCTTCCTTCCCTGACAGCTATGGGAAGATGGAACCCAGTCCAGGCCTTGAGTGCA
>9:5000-6000
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
gffread
gffread, from Cufflinks / StringTie, is another option and it can output coding or non-coding strand sequence. I go over this, here: A: Cufflinks gffread utility
Kevin
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