Details
-
Type:
Task
-
Status: To-Do (View Workflow)
-
Priority:
Major
-
Resolution: Unresolved
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:10
-
Epic Link:
Description
Task: Create a new IGB app titled Summits to FASTA.
Details: The highly used bioinformatics program MACS produces a bed file called NAME_summits.bed (see attached example). This file is useful for identifying important regions in the genome. However, it only provides the location of those regions, and not the genomic sequence. The genomic sequence is often needed for downstream bioinformatics analysis. Therefore, the Summits to FASTA app will use as input the NAME_summits.bed file to create a FASTA file containing the nucleotide sequence for each region from the NAME_summits.bed file. This will require accessing the sequence from the .2bit genome sequence file provided by the currently loaded genome in IGB (i.e. the user will need to have loaded a genome in IGB for this app to work correctly).
Input: NAME_summits.bed
Output: NAME_summits.fasta