Hello everyone, I am a beginner in bioinformatics, and asking for help. I got a .bed file generated from segemehl software, there is chr name and splice site (two coordinates) and other information, now I want to add gene description (or just gene name) to each splice event (back-splice), is there any software or command can I use to achieve the goal? many thanks!
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donger1103 •
One option is to use BEDOPS bedmap and convert2bed to map annotations to mapped reads.
Here is one command demonstrating how to do just that with GFF-formatted annotations:
$ bedmap --echo --echo-map-id-uniq your_mapped_reads.bed <(gff2bed < your_annotations.gff) > answer.bed
The file answer.bed contains each read along with the ID values ("name") of any overlapping annotations.
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Alex Reynolds
It really works! thanks a lot for your kind help:)
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donger1103 •
You're very welcome!
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Alex Reynolds
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Have a look at
bedtools intersect(or maybebedtools closest), there's likely an option to have it print the whole line when you intersect the BED file with the GFF/GTF file describing your organism.thanks for your help, I will try to learn the usage of bedtools:)