FuLeTA
Tookit 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
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Transcript isoform diversity analysis
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Alternative splicing events
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Comparison to known transcriptome annotation
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Co-occurrence of alternative RNA processing events analysis
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ORF diversity analysis
Installation
- Operating system requirement: any OS running perl (>= 5)
- Download the toolkit:
git clone https://github.com/sunlightwang/FuLeTA.git
- 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
- 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