rsalz
commented
7 months ago found out the hard way that the problem was that my gtf annotation was zipped. Please put in a warning that all files used as input for this program should be unzipped
Closed rsalz closed 7 months ago
rsalz
commented
7 months ago found out the hard way that the problem was that my gtf annotation was zipped. Please put in a warning that all files used as input for this program should be unzipped
Hi! I am using TERRACE, which works great with STAR aligned reads. In my STAR command, I have chimeric mapping enabled, which I suspect helps TERRACE detect circRNAs. I used the same reads to align using hisat, and I get a blank output file after TERRACE runs to completion (no errors).
On the main readme, it says you can use a bam from STAR OR HISAT2 as input, but I was wondering if TERRACE has actually ever been tested with hisat2 aligned reads? I see your example data is also from STAR.
It would be great if you could provide some context about what aligners and corresponding settings for the aligners work with TERRACE, because it doesn't seem to be all of them.
Eventually, more informative output or a log file should be provided because I don't know why I have an empty file. I once had an empty output because I used two different versions of the genome (chr1 vs 1), and I had to figure that out myself.