I had a problem with the example command not working because of a malformed file: docs/GRCm38/GRCm38.sizes. First of all this file doesn't end in a newline, which by itself can cause problems. The main problem though is that there is a rogue whitespace character causing bedtools to complain:
Less than the req'd two fields were encountered in the genome file (/home/andy/FAST-iCLIP/docs/GRCm38/GRCm38.sizes) at line 22. Exiting.
I fixed this with a simple awk 'BEGIN{OFS="\t"}{print $1, $2;}'.
I made sure all your annotation text files ended in newlines with:
But as I said, the problem with the .sizes file was something else. I still encourage you to check that there aren't errors in the tabs/whitespace in the tab-delimited annotation files.
I had a problem with the example command not working because of a malformed file:
docs/GRCm38/GRCm38.sizes. First of all this file doesn't end in a newline, which by itself can cause problems. The main problem though is that there is a rogue whitespace character causing bedtools to complain:I fixed this with a simple
awk 'BEGIN{OFS="\t"}{print $1, $2;}'.I made sure all your annotation text files ended in newlines with:
But as I said, the problem with the .sizes file was something else. I still encourage you to check that there aren't errors in the tabs/whitespace in the tab-delimited annotation files.