Entering edit mode
8.2 years ago
chaoyuan
•
0
I have three BED files generated by QuEST. They are triplicates and I hope to find common peaks that I'll send to HOMER for further analysis.
I first tried "homer mergepeaks" with the three files it would seem that it'll take an entire week to finish the process. (Each file contains more than 15 million peaks), so I stopped it after two days..
Then I tried "bedtools multiinter", which took just around 5 minutes to finish.
My question is : Can I use the results from the two methods interchangeably?
You need check exactly what both are doing on a small subset of data, given that at larger picture both may look doing the same job but are not the same. If homer is taking long time, split the peaks by chromosomes or any other criteria ( like multiple windows) and run in parallel.