Help interpreting Stringtie 'fully covered transcripts' output

Question

[freuv]

I ran Stringtie on RNASEQ data with the -c option, which produces a list of reference genes that are covered end-to-end by reads from your run.

However, I am having some difficulty interpreting the output.

Specifically, there are multiple entries for the same Ensembl ref annotation and I'm not sure why that is:

1   ensembl_havana  mRNA    4807823 4846739 .   +   .   ID=ENSMUST00000027036   CDS=4807914 4845014 geneID=ENSMUSG00000025903   gene_name=Lypla1
1   ensembl_havana  exon    4807823 4807982 .   +   .   Parent=ENSMUST00000027036           
1   ensembl_havana  exon    4808455 4808486 .   +   .   Parent=ENSMUST00000027036           
1   ensembl_havana  exon    4828584 4828649 .   +   .   Parent=ENSMUST00000027036           
1   ensembl_havana  exon    4830268 4830315 .   +   .   Parent=ENSMUST00000027036           
1   ensembl_havana  exon    4832311 4832381 .   +   .   Parent=ENSMUST00000027036           
1   ensembl_havana  exon    4837001 4837074 .   +   .   Parent=ENSMUST00000027036           
1   ensembl_havana  exon    4839387 4839488 .   +   .   Parent=ENSMUST00000027036           
1   ensembl_havana  exon    4840956 4841132 .   +   .   Parent=ENSMUST00000027036           
1   ensembl_havana  exon    4844963 4846739 .   +   .   Parent=ENSMUST00000027036

[h.mon]

Seems different exons of the same transcript.

[freuv]

Would this suggest that there are alternatively spliced transcripts of the same gene present?

Answer 1

[h.mon]

The option you are referring to is -C, not -c. As I said in my comment, the output you are showing are just the exons that constitute the transcript ENSMUST00000027036.

Would this suggest that there are alternatively spliced transcripts of the same gene present?

No, the output you have shown does not suggest alternative spliced transcripts - it doesn't preclude it also, because you have shown just a small snippet. You have to search for different transcripts of the same gene to see if there is evidence of alternative splicing. For this particular gene, grep "gene_name=Lypla1" cov_refs.gtf would tell if there is evidence for alternative splicing or not.