problem in provided annotations

[andypohl]

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:

$ find docs/ -type f -exec file '{}' \; | grep ASCII | cut -f1 -d':' | xargs sed -i -e '$a\'

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.