Has anyone tried uploading a .txt tab-delimited file as an interval file and noticed that setting the attributes does not work as it did before the Galaxy update?
- I uploaded a .txt tab-delimited file as an interval file (headers: gene, locus, chrom, chromStart, chromEnd). In the preview, the data sorts nicely into 5 columns.
- I tried saving the following Attributes: comment lines = 1, chrom = 3, start = 4, end = 5, strand column (unchecked), name identifier column = 1.
- Then when I clicked Save, the strand column box checked itself.
- I unchecked both the Strand and Name Identifier (as an experiment) and clicking save re-checked both boxes.
I attempted to fix the problem by uploading a version of the file that has a strand column (headers: gene, locus, chrom, chromStart, chromEnd, strand). After setting the strand column to "6" I tried to run Join (under Operate on Genomic Intervals) with some ChIP intervals. The process keeps gettign stuck and I get no error messages.
Please help. Thank you.