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.
4 answers
The first few lines of the file I am trying to sort are:
chr8 47953244 47954244 chr8:47953244-47954244 peak 1 chr5 143584660 143585660 chr5:143584660-143585660 peak 2 chr15 38472011 38473011 chr15:38472011-38473011 peak 3 chr5 38738013 38739013 chr5:38738013-38739013 peak 4
The output file I get after sort is simply a blank file. There is no text.
Sorry about that, and I've checked that the file is converted to ASCII text.
chr8 47953244 47954244 chr8:47953244-47954244 peak 1
chr5 143584660 143585660 chr5:143584660-143585660 peak 2
chr15 38472011 38473011 chr15:38472011-38473011 peak 3
chr5 38738013 38739013 chr5:38738013-38739013 peak 4
chr4 128963983 128964983 chr4:128963983-128964983 peak 5
Your bed file seems to be separated by space instead of tabs. You can try this:
gsort -t' ' -k1,1V -k2,2n in.bed >out.bed
EDIT: Adding to Alexander's command - to sort the first column correctly, you will need to add a -k1,1V. The updated command should now work for your file.
$ cut -d' ' -f1,2,3 test.txt | gsort -t' ' -k1,1 -k2,2n
chr15 38472011 38473011
chr4 128963983 128964983
chr5 38738013 38739013
chr5 143584660 143585660
Adding -k1,1V
$ cut -d' ' -f1,2,3 test.txt | gsort -t' ' -k1,1V -k2,2n
chr4 128963983 128964983
chr5 38738013 38739013
chr5 143584660 143585660
chr15 38472011 38473011
You can add -u to keep unique rows
Just as recommendation by experience: Do not use the bedtools sort function. Use either the built-in sort of OS X or (my recommendation) get gsort from GNU coreutils, e.g. via homebrew, which provides a multithreading option. gsort in my experience outcompetes both other options.
bedtools sort is slower and consumes more memory than built-in sort, see also the manual page of bedtools, where this is mentioned: http://bedtools.readthedocs.io/en/latest/content/tools/sort.html GNU command would be
gsort -k1,1 -k2,2n with --parallel=cores and -u to keep only unique entries, if desired.
I have gotten it to do what I want now. First I convert to unix format using
changeNewLine.pl unixfile.txt and check that it has been converted,
file unixfile.txt gives me: unixfile.txt: ASCII text
Then I was able to sort using the same command I was using before which works now:
sort -k1,1 -k2,2n unixfile.txt > unixsort.txt
The only thing different I did was to open up the txt file in excel and save it again as a txt. This allowed changeNewLine.pl to work which wasn't working before for me. Maybe the computer is being moody or maybe I overlooked something basic, but thank goodness it finally works. Thank you everyone for the advice and your time, it was truly appreciated.
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mac2unix. Just run it like this:mac2unix file.txt. That will convertfile.txtin place.Hi Sadia. The
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