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.
Thanks
On Search I find that, If the format is ELANDMULTIPET, user must provide two treatment files separated by comma, e.g. s_1_1_eland_multi.txt,s_1_2_eland_multi.txt.
I have only one paired reads mapped file. So how do i proceed?
Hello,
This is the same exact issue that we identified yesterday. There may be a tool form input problem or mix-up between the two formats (ELANDMULTIPET vs ELANDMULTI). Our team discussed this briefly and I created a Trello card that you can follow for the resolution.
For now, to use paired-end data, a local or cloud Galaxy with the MACS version 2 tool (from the Tool Shed http://usegalaxy.org/toolshed) is the best solution we can offer.
Thanks for reporting the issue! Jen, Galaxy team
Thanks Jennifer. I tried to install MACS2 using the link https://toolshed.g2.bx.psu.edu/. I was not successful and this is the error report which I get even after enabling third-party cookies in my browser. Please advice.
Repository installation is not possible due to an invalid Galaxy URL: None. You may need to enable third-party cookies in your browser.
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, Ismail
Thanks for clarifying. We are looking into this more and will get back to you shortly.