I have bed files (from an ENCODE eCLIP experiment) in the format below.
I need to obtain a gene list from the chromosomal coordinates.
I have tried Galaxy: using USCS table browers KnownGene and kgXref functions, and join operations, but the gene list I get has clearly been duplicated in some way as some genes have the correct number of eCLIP tags, and some have thousands more than are evident when I view the .bed file in IGV.
has anybody got a simple, up to date way or solving this. I do not code so simple explanations if possible. Previous workflows in galaxy have not worked.
Thanks in advance!!
chr7 155100450 155100506 rep02 1000 + 4.49254608837777 22.7294143201152 -1 -1
chr7 155100424 155100441 rep02 1000 + 3.74937915504325 15.3042207236355 -1 -1