imeter
2022 reboot of IME project. Starting over from the beginning with Python.
Data
The at_ime_master.gz file contains information about most introns in the A.thaliana genome (copied from KorfLab/datacore/project_imeter).
The file is tab-separated and has the following columns
- Transcript ID
- Intron begin relative to start of gene
- Intron end relative to start of gene
- Strand of the gene in the genome
- 11 expression values (RNA-seq splice junctions) for various tissues
- Aerial
- Carpel
- Dark Grown Seedling
- Light Grown Seedling
- Leaf
- Pollen
- Receptacle
- Root Apical Meristem
- Root
- Shoot Apical Meristem
- Stage 12 Flower
- Sequence of the intron
The file looks like this (4 lines shown of 142,779):
AT3G02220.1 1057 1151 - 380 349 601 2717 3010 3 489 321 1010 49 499 GTAAGCTTCTCTAGTTACTTTGAAGAGTTTTTGAGATTTGTAAATGTGTATGTTTGTGTGATTTGGTCCTGAAGTTGCGTATTTGCTTGACATAG
AT3G02220.1 914 1008 - 362 302 677 2889 3291 0 462 373 1170 9 655 GTTTGTCTTTTAATTATTCCGCTTTTGGCTTCTAATGTTCAATTTCATGCTTGTTTTTGGGAGGTTGTTGCTGATTTCTTATTGATGTGATGCAG
AT3G02220.1 753 870 - 331 309 542 2861 2968 2 504 340 839 48 503 GTACTTGTACCTTGAAGACAGTCTTTCTTCTACTTATGCTAGATGCTGGTTTCCTTAAGAGTGGGTTTAGTAGACAAGATATTAAACTAATCTTGAGGTAATTATTCGTTTCTCGCAG
AT3G02220.1 565 688 - 283 249 571 2568 2308 5 471 374 697 25 265 GTTAGTGTTTTCTTTCTTTGCTTTTGTTCTCGTACTTTCTTGGCTAATTAGAGTGTATAGATCAGTATCTTGTTTTATAAGTTGATGTGTTATGGTATTGAAATGGGTATGAAACTGATAACAG
Version 1
The v1 directory contains a reimplementation of IMEter version 1.0 as published. The results will be a little different because the training set for the original version is different from the at_ime_master.gz included in the data directory.
Version 3
The v3 directory contains some ideas of a better implementation of IMEter 1.0. It is not a follow-up of version 2.0. Some things to address in version 3:
- Counting of both strands.
- Not splitting the data set into proximal and distal. Instead, use a proximal weight based on distance. Distal weight is 1 - proximal.
Notes
- Leaf tissue is where the original experiments were done
- Something with tissues in the next experiments?
- Deal with alternative isoforms somehow