BT-FLOR: Build Transcripts From LOng Reads

The software build transcripts from long reads.

The software get bam file as input and output gtf file with all alternative spliced transcripts and exons that declared by average of mapping positions of close reads.

The gtf also contain the counts of read in each transcript.

Optinally user can supply known gtf file. In this case the gtf also contains the percent of overlap between the known gtf to the closest transcript and exon that found by the BT-FLOR.

• Installation
  • Requirements
  • Installation BT-FLOR package
• User guide
  • Run pre-process the input bam file
  • Run the main program
• Releases
• Source code
• The algorithm
  • Input file
  • Step 1 - grouping read according start mapping position and finding their average position
  • Step 2 - finding average of each start and end edges of the exons in the group from step 1
  • Stranded protocol
  • Step 3 - build transcripts
  • Output
  • Step 4 (optional) - intersection with known gtf

License

BT-FLOR is licensed under GNU General Public License version 3. License needed for commercial use.

Author

Refael Kohen,

refael.kohen@weizmann.ac.il, refael.kohen@gmail.com

Bioinformatics unit at Life Sciences Core Facilities (LSCF)

Weizmann Institute of Science, Rehovot 76100, Israel.