bedtools getfasta concatenating sequences

bedtools getfasta concatenating sequences


Hi, I have a bed file containing exons of the genes. the name field is specified with name of the gene like (ENSG***). when I run bedtools getfasta I get the sequences of each exon separately. is there a standard way in order to concatenate sequences that have the same gene name? or I should write a script to do this manually on the fasta files.
when I read the bedtools documentation there is a -split switch which is only applicable to bed12 file format. link but my bed files are not bed12.
Thanks in advance




Read more here: Source link