Missing bed_to_juncs function

[Leo Creasey]

Hello

I am running a RNA-seq pipeline, and I am at a stage to filter SNPs. I have a junctions.bed file and I am trying to determine SNPs near splice sites. Following a walkthrough of the process, I have gotten to this point:

>bowtie2-inspect -s n_vitripennis | tail -n +4 | cut -f 2- > genome_size.txt 

>cat junctions.bed | bed_to_juncs | flankBed -g genome_size.txt -b 1 | slopBed -g genome_size.txt -b 5 > windows.bed

When I run the second line, I get the error:

bed_to_juncs: command not found. 

Is it the case that bed tools has removed this function? And if so is there a replacement function/wait navigate this issue?

Kind regards

Leo Creasey