From: Michael Wilson <michael.d.wilson@gmail.com>

Date: January 26, 2010 12:43:30 PM EST

To: Anton Nekrutenko <anton@bx.psu.edu>

Subject: Re: [galaxy-user] GALAXY Question

Dear Anton,

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.

1) can you use Base Coverage on interval files?
2) 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.

Best regards,

Mike