Hello, I sort of have 2 questions. I've always used bedtools through cygwin on my PC but have recently switched to a MAC. It took me a while to get used to the line endings issue with txt files on the MAC and even though everyone recommends mac2unix to convert files, it always gives me blank files even though I have the dos2unix package installed. So even though I would prefer mac2unix, I am stuck with using "perl -p -e 's/\r/\n/g' < macfile.txt > unixfile.txt".
In addition, I am currently trying to use the sort function from Bedtools. sort -k1,1 -k2,2n input.bed > sortedinput.bed
and when I do not specify an output filename, I can see the sorted results in the Terminal but when I want to the results to go into an output file, the file is just blank. The exact command I am using is "sort -k 1,1 -k2,2n unixfile.txt > unixfile-sort.txt"
Could someone please offer up any ideas and or issues of how to make sort/bedtools work for me and any issues I may not have addressed when switching between PC and MAC. Thanks.