Cuffcompare Class Code "U" Transcripts

Question

[upendrakumar.devisetty]

I thought cuffcompare class code "u" transcripts are novel. But when i blasted those class code "u" transcripts against reference annotated transcriptome i found ~20% to have hits. Can somebody explain me why?

Answer 1

[Istvan Albert]

It all depends on the interpretation of the words novel and that of getting blast hits.

A previously unannotated transcript may very well be partially identical to an annotated one. Blast performs local alignments.

[upendrakumar.devisetty]

Does that mean that cuffcompare intrepreted those transcripts as wrong? My final aim is to validate some of the class code u transcripts to make sure they are not present in my reference transcriptome and i am wondering now is it ok to exclude those 20% transcripts for validation purposes?

[Istvan Albert]

Getting hits with blast does not mean the transcripts are identical (you are most likely getting local alignments). Make sure to check that first.

Answer 2

[upendrakumar.devisetty]

Hi Albert,

Yes you are right!

I just multiple alignment of one of "u" transcript with the annotated gene that it it and blast alignment is very scrappy here.......

TCONS_00003593      ----CTCCTCCT---------CCT-------------TT------TTCC----------- 17
Bra040786           ATGTTTGCTGCTGGTGAAGAACCCAACGACGAGAGGGTTAATACGTTCCACAAACCGAAG 60
                         * ** **         **              **      ****           

TCONS_00003593      -----------CGTCTT---AGTTTTGAGCTCTGA------TCAATTCCTCCCT------ 51
Bra040786           AGAATCGAAACCATACTCGAAGCTTTAAATCCAGAGGAGACTCAACTTGTGTTTATGGTG 120
                               * *  *   ** *** *   * **      **** *  *   *      

TCONS_00003593      ----TTC--------------GTCGT----CATTAGCTCAT--GCCATCCCTCCT-CCAG 86
Bra040786           GCAGTTCCTCAGATTAAAGAGGTTGTTTCACAGTGGCTCTTTGACCCTCTCTCCAGCCAG 180
                        ***              ** **    ** * **** *   ** ** ****  ****

TCONS_00003593      TCC----------------TCCTTATGG-TATAGTTGGTG-ATGGATATATCATCA---- 124
Bra040786           TTCAAGACCTTCGCCAACGTCTTCATTGCTGTCGTCGGCGCGGGGGTTCTTGGTCTTCCT 240
                    * *                ** * ** * * * ** ** *   ** *   *  **     

TCONS_00003593      -ACGC-TTCTAGCTTACT---CAGCTCCCGCTTGGGCAAGCT-------------TTATG 166
Bra040786           TACGCCTTCAAGCGCACAGGATGGCCCATGGGTGGGGAAGGTAGGACCATTGAGTTTATG 300
                     **** *** ***  **      ** *  *  **** *** *             *****

TCONS_00003593      -----GCCGGTCC-------TTTTTTGATTCTCCCCCT---------------------- 192
Bra040786           CAACGACAAGGCCGCAAGAGCTTTAAGACTCCCCTCTTACTAGATCACAACGATGATAAG 360
                          *  * **        ***  ** ** ** * *                      

TCONS_00003593      ------------CTCCCTTTCCTTGT--ATCTTGTCTTCGATCTCC----------TTTC 228
Bra040786           GGAACTATTAAACATCCTTTCCCTATGAATCTTTTCTTAAAACCCTGGAGGCTCAGTCAC 420
                                *  ******* * *  ***** ****  * * *           *  *

TCONS_00003593      TGCTTA---CAAG-----AACCCTG------------AGGAGCAAATGTTTTTGATTG-- 266
Bra040786           TGGTTCTATCAAGTTGTTAAGTTTGGTATCGTTCAATATAAGGGTATTGCTTCGGTTGTT 480
                    ** **    ****     **   **            *  **   **   ** * ***

TCONS is my cuffcompare "u" transcript and Bra is the gene that it hit.