Must the GTF file used by stringtie be the same as the GTF file used by aligner?

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq

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Must the GTF file used by stringtie be the same as the GTF file used by aligner? #334

Open ZHIDIHUAYUAN opened 3 years ago

ZHIDIHUAYUAN commented 3 years ago

Hi, I have bam files aligned with STAR 2- PASS using the GENCODE fasta file and GENCODE annotation file. Then I want to assemble transcripts using the Refseq annotiation because there are some attributions I need.

Can the GTF files used by stringtie be different from the one used by STAR?

Thank you.