I'm using bedtools getfasta to get a bunch of sequences from chromosome 1. I have "chr1.fa" (from UCSC Genome Browser) as the input fasta file, and I have a BED file with chromosome location, start, stop, and name columns. My input looks like this: bedtools getfasta -fi chr1.fa -bed bedfile.bed -fo testing.fa.out -name because I'd like to organize the sequences by name.
The problem is this: when I run this command I don't get any errors, it just outputs a blank file with whatever name I gave it (in this case testing.fa.out). The problem may come down to this: I was given an excel spreadsheet with coordinates on it and I simply saved the file as tab-delimited text format. I copied out the three relevant columns- chrom, start, and stop- and put them into a new spreadsheet before saving it as a tab-delimited text file. Then I gave the columns each a name. It looks like in the tab-delimited text file the "tabbing" is different for the first 100 or so lines; the distance between columns is shorter. Then, later, the spaces between the columns become wider. If this is the problem, how can I fix this? I'm on a Mac, if that's relevant information.