For paired-end analysis, why do i see Chip-Seq Tag file 1 and 2. ? Both forward and Reverse reads were mapped to the reference genome and the resulting filtered reads contain only one file. So what two type files should be added? please suggest.
Which tool are you using? And what Galaxy server are you working on? (If your own, you can reference the tool by the Tool Shed repository link). Thanks - this info will help us to offer advice. I see the other comment, but we can address/incorporate that in the next step. Best, Jen, Galaxy team
In Galaxy, I am using NGS peak calling MACS tool. The tool requires elandmulti format for paired-end data and I have converted my Filter SAM data file accordingly. in subsequent steps, the tool request for Chip-Seq Tag file 1 and Tag file 2 and I have only one paired-end mapped files. In short my question is, what should I add for Tag file 2? Pls suggest.
Thanks for clarifying. We are looking into this more and will get back to you shortly.