bedtools

bedtools is a toolkit for comparing and manipulating genomic interval files. In this module, bedtools identifies overlapping regions between a query interval file and a reference annotation file.

Workflow

1. Input interval files
   Upload two genomic interval files: a query file and a reference file.

2. Run interval intersection
   Use bedtools intersect to find overlaps between the query intervals and reference intervals.

3. Retain overlap records
   Export overlapping query and reference records using the -wa -wb option.

4. Summarize overlap results
   Report the number of query records, reference records, and overlapping records.

Data

The bedtools sample dataset contains test_variants.vcf as the query interval file and test_genes.gff as the reference annotation file. It is used to demonstrate how variant positions overlap with annotated gene regions.

Result

v0.2: The pipeline is stored in Code Repository: CRS1245479389064605696. The computational docker enrionment is stored in Software Repository: SRS1245481913934950400.

Reproducibility

The pipeline utilizes code CRS1245479389064605696 and Docker image SRS1245481913934950400, both of which are stored in the BMAP repositories.

Usage

1. Select the application 'bedtools'
2. Click on the 'Analysis' button
3. Click on the 'Metagenomics pipeline'
4. Fill in the request parameters

5. Upload the compressed data in gz or rar format.