Cufflinks merge not report Transcripts?

Question

[MarVi]

Hello everyone,

I modify the question. It still being related to Cufflinks.

Does someone know why when cufflinks merge is used, only the exons are reported? Why the transcripts are not associated? As on the output of cufflinks algorithm.

CuffMerge

GL000205.2  Cufflinks   exon    54409   56709   .   -   .   gene_id "XLOC_000024"; transcript_id "TCONS_00000024"; exon_number "1"; oId "CUFF.24.1"; tss_id "TSS24";
GL000205.2  Cufflinks   exon    56802   58312   .   -   .   gene_id "XLOC_000025"; transcript_id "TCONS_00000025"; exon_number "1"; oId "CUFF.48.1"; tss_id "TSS25";
GL000205.2  Cufflinks   exon    60222   60360   .   -   .   gene_id "XLOC_000025"; transcript_id "TCONS_00000025"; exon_number "2"; oId "CUFF.48.1"; tss_id "TSS25";
GL000205.2  Cufflinks   exon    63563   63759   .   -   .   gene_id "XLOC_000025"; transcript_id "TCONS_00000025"; exon_number "3"; oId "CUFF.48.1"; tss_id "TSS25";
GL000205.2  Cufflinks   exon    56802   58312   .   -   .   gene_id "XLOC_000025"; transcript_id "TCONS_00000026"; exon_number "1"; oId "CUFF.48.2"; tss_id "TSS25";

Cufflinks

chr1    Cufflinks   transcript  347982  348366  1000    -   .   gene_id "ENSG00000236679.2"; transcript_id "ENST00000458203.2"; FPKM "0.0299041492"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.137559"; cov "0.056163"; full_read_support "yes";
chr1    Cufflinks   exon    347982  348366  1000    -   .   gene_id "ENSG00000236679.2"; transcript_id "ENST00000458203.2"; exon_number "1"; FPKM "0.0299041492"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.137559"; cov "0.056163";
chr1    Cufflinks   transcript  257864  264733  1   -   .   gene_id "CUFF.1"; transcript_id "ENST00000442116.1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.026540"; cov "0.000000"; full_read_support "no";
chr1    Cufflinks   exon    257864  259025  1   -   .   gene_id "CUFF.1"; transcript_id "ENST00000442116.1"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.026540"; cov "0.000000";

Thanks in advance, if somebody has a clue to share with me.

MaVi

[lakhujanivijay]

Hello MarVi,

You should know that the old 'Tuxedo' pipeline of Tophat(2) and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using salmon.

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

[MarVi]

Hi Vijay,

Thank you very much for your nice response and advice! Actually, I have been using both StringTie and Cufflinks for transcriptome reconstruction, (Alignments are made with STAR.) Then, I have noticed that StringTie is quite fast compared to Cufflinks and it reports 'fairly' enough number of transcripts. However, I wanted to see if the results were similar between both. Surprisingly Cufflinks reports twice more the number of transcripts. Trying to figure out why of this and to take a decision of which I should use, I noticed this 'issue' when using cuffmerge.