Hello,
I ran the MACS2 on my merged bam file in galaxy and it generated a bed file. The bed file had 4 sub files - file.fli, file.bedstrict, file.tabix and file.bigwig. It showed an error while generating file.bigwig but it is not specified. I have to visualise this narrowpeak file in IGV. I can see chipseek-like peaks on a broad genome view but when i zoom into a particular chromosome i can only see the small bars. How can i fix this ?
Welcome @anushree
The outputs you describe seem a bit odd to have been produced by Galaxy. Would you like to compare to this simple run I just created?
Other than that, in order for IGV to have base-level resolution for any input, any format, the database key needs to be set in IGV and your file from Galaxy needs to have that same database key assigned. This prior topic explains, and you can ask questions if this is your issue.
The example in my shared history above will link to IGV anywhere since the database key was hg19 and this is already known by IGV. If you need a custom key instead, this isn’t overly complicated, we can explain how, and you only need to do this set-up once per-custom genome, then you can assign the key to more data later on to visualize it in that same browser.
We can follow up more. Maybe share your history along with some screenshots for what you are seeing in IGV. With both of those we should be able to pin-point exactly what is going on. 
Thank you for taking the time to reply ! but I used the UCSC genome browser from the visualise section and I got the result with proper peaks.
Hello,
I was able to visualise the narrowpeak file in UCSC genome browser, but the error while generating a bigwig file still persists. I have attached a picture below. Will this change anything in my visualisation and what exactly does this error mean ?
Hi @anushree
I’m glad that your genome (hg38) was supported by UCSC, since that’s the easiest way to view this data, plus you can save it in a Session (truly useful context saving feature!).
This is a file format conversion error, and it won’t impact any of the other green datasets but it might impact how the top level dataset is consumed by downstream tools that are expecting to use the bigwig version of the data.
Try using the re-run icon on the red dataset to see if that is enough to clear this up.
If this is not enough, please consider sharing your history back containing the error and I’ll take a closer look. We have some known issues with certain file conversions right now, and I’ll be able to confirm plus share this with our other administrators. BUT – some of those corrections are rolling out, more everyday, so a rerun is worth a try first. How to generate a history share link is in the banner of this forum. 