Tool:Bedsect: An integrated web server application to perform intersection, visualization and functional annotation of genomic regions from multiple datasets

Question

[Prakash]

Hi,

We have made an naive attempt to build a tool that could be highly beneficial for users working in the area of genomics. We have developed an web server application Bedsect to perform intersection of genomic regions from multiple datasets.

Currently available features.

1. BED file overlap.
2. Generate UpSet and correlation plot for genomic region overlap.
3. Functional annotation using GREAT.
4. Direct link to upload BED files to UCSC genome browser.
5. Download unique as well as overlapping regions for futther downstream analysis

Please use this tool and provide your suggestions to enhance or improve this tool.

[ATpoint]

May I ask about your initial motivation to develop this application? Well-maintained solutions like Galaxy that include BEDtools intersect operations do already exist. Just wondering.

[Prakash]

Well, Galaxy is indeed a great platform that provides users to select tools to perform specific task. In case of BED files overlap, multiple other analyses can be performed like functional annotation of intersecting regions locating regions in genome browsers for and extracting regions for primer design in case of ChIP qPCR . Moreover, users would also like to have quick visualization of subset of intersecting regions in terms of numbers and correlation between multiple BED files as well. So, basically our motivation was to develop an integrated user friendly platform where users can just upload their BED files and perform these analyses in one go.

Thanks