FuLeTA

Toolkit for full length transcriptome annotation analysis, including isoform diversity, alternative splicing among transcripts, comparison to known transcriptome, splicing coupling, and their consequences on ORF diveristy.

• This is part of the rat hippocampus transcriptome annotation project, where hybrid sequencing technology (PacBio + Illumina) was applied to get full-length transcriptome landscape for rat hippocampus.
• All the executables of different functions are based on the exon block analysis, which is very useful in comparison of isoform structure annotation.

Content

1. Transcript isoform diversity analysis

2. Alternative splicing events

3. Comparison to known transcriptome annotation

4. Co-occurrence of alternative RNA processing events analysis

5. ORF diversity analysis

Installation

1. Operating system requirement: any OS running perl (>= 5)
2. Download the toolkit: git clone https://github.com/sunlightwang/FuLeTA.git
3. Changed to the FuLeTA directory and run the scripts: cd FuLeTA

Expected time: a couple of minutes

Usage

• IsoDiv.pl
  Description: Comparing each isoform to its nearest isoform in the annotation collection
  Usage: IsoDiv.pl <isoform.refflat> <isoform.refflat w/ results in an additional column>

• IsoPairwiseCmp.pl
  Description: Pairwise comparison for isoform differences in the same gene locus
  Usage: IsoPairwiseCmp.pl <isoform.refflat>

• cmpIso2known.pl
  Description: Comparing one collection of transcript isoforms to an existing (e.g. RefSeq) collection
  Usage: cmpIso2known.pl <new_collection_isoform.refflat> <known_isoform.refflat> <new_collection_isoform.refflat w/ results in an additional column>
  Note: The comparison results would be useful for investigating co-occurrence of alternative RNA processing events

• cmpORF2known.pl
  Description: Comparing one collection of open reading frames (ORFeome) to an existing (e.g. RefSeq) collection
  Usage: cmpORF2known.pl <ORF.bed> <known_ORF.bed> <ORF.bed w/ results in an additional column>

Examples

• IsoDiv.pl

IsoDiv.pl example_data/FLT.rn6.chr15.refflat example_data/FLT.rn6.chr15.IsoDiv   

• IsoPairwiseCmp.pl

IsoPairwiseCmp.pl example_data/FLT.rn6.chr15.refflat example_data/FLT.rn6.chr15.IsoPairwiseCmp   

• cmpIso2known.pl

cmpIso2known_v2.pl example_data/FLT.rn6.chr15.refflat example_data/RefSeq.rn6.chr15.refflat example_data/FLT.rn6.chr15.cmpFLT2RefSeq   

• cmpORF2known.pl

cmpORF2known_v3.pl example_data/FLT.rn6.chr15.bed example_data/RefSeq_CDS.rn6.chr15.bed example_data/FLT.rn6.chr15.cmpFLTORF2RefSeq  

Expected time: a couple of minutes

Contact

xi (dot) wang (at) dkfz (dot) de
for bug reporting or requiring additional functionality

Citation

1. Xi Wang, Xintian You, Julian D. Langer, Jingyi Hou, Fiona Rupprecht, Irena Vlatkovic, Claudia Quedenau, Georgi Tushev, Irina Epstein, Bernhard Schaefke, Wei Sun, Liang Fang, Guipeng Li, Yuhui Hu, Erin M Schuman, Wei Chen. Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus. Nat Commun 10, 5009 (2019) doi:10.1038/s41467-019-13037-0