The transcript_version is attached to transcript_id in the gtf file I was using:
chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
chr1 HAVANA transcript 11869 14409 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1 HAVANA exon 11869 12227 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
It is strange because the transcript_version is together with the transcript_id in the transcriptInfo.tab file in the genome folder, but the transcript_version is missing in the Aligned.toTranscriptome.out.bam.
A few lines of the transcriptInfo.tab:
198093
ENST00000456328.2 11868 14408 14408 1 3 0
ENST00000450305.2 12009 13669 14408 1 6 3
ENST00000488147.1 14403 29569 14408 2 11 9
ENST00000619216.1 17368 17435 29569 2 1 20
ENST00000473358.1 29553 31096 29569 1 3 21
ENST00000469289.1 30266 31108 31096 1 2 24
The Log.out file from the genome generation is attached and I was using STAR_2.5.1b_modified. Thanks a lot!
Best regards,
Kaiyang