Forgive me, I know this question has already been asked but I ran into a few problems while trying the given methods.
So I have this text file in this format:
CACAAAGATAAAGACTTAATTAAAAACC 47564052 47564079 + -28.27 P CACAGTAATGAATGACTTTGCAAAGATT 47425208 47425235 + -29.10 P CACTGTGGTCTGCACCCTTGGTGAAATA 47344215 47344242 + -29.13 P CACTGAGATAAATGCAGCAACCTAAATT 47444207 47444234 + -31.09 P CACCCATGCACACCCCTCCGCACAAACA 47556633 47556660 - -31.41 P
Note: there aren't actually spaces between lines it was just easier to read on Biostars if i put them here.
The first methos I tried was using
> cut -f 2,3,4 cadm1.txt >cadm1.bed
However, I cannot open the bed file in genome browsers such as IGV and IGB.
I also have tried using GenomeIntervals2BED
python SeqGI_V1.2/scripts/GenomeIntervals2BED.py -f testfiles/cadm1.txt -c 2,3,4 --cID=1 -o testrun/cadm1.bed
but keep getting "ERROR: column position (ID) has to be an integer." even though I have tried putting every column into cID ie. cID=1, cID=2 etc.
Please explain in simple terms as I am pretty new to any type of coding.