Do you mind sharing your history with me (firstname.lastname@example.org) so that I can take a look at what might be going on?
I have a question regarding the 'Base Coverage' function. I have a 9 column interval file and when I perform 'Base coverage' it reports 0 bp of sequence despite there being many intervals. If I convert the same file to a bed file and then perform 'Base Coverage' I get the correct number of basepairs. There does not seem to be any problem with my interval files. I was wondering if this may be a bug.
As I would like to use 'Base Coverage' in one of my workflows I tried to get around this problem by converting my interval files to bedfiles with 1:chrom 2:start 3:end (I do not indicate strand or name in these bedfiles). However when I use Filter and Sort: Select > ^chr21 , the new bedfile which is created with only lines starting with chr21 has for some reason had column 6 replaced with '+' and is labelled as 'strand' and column 8 is labeled with 'name'. I am not sure why the bedfile changes format after using the select command and if this is intentional or if you know a way around this happening.
- can you use Base Coverage on interval files?
- is there a way to avoid changing the column designations in a bedfile when using Filter and Sort: select.
Thank you again for all your help and excellent resources.