i want to know when i am doing stringtie and uploading GTF file of zebrafish genome its giving error or not matching notations with hisat2 in built genomic sequence, help me find zebrfish gemome GTF file that matches to european galaxy in built zebrafish genome
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For your followup question @poojashukla about the predicted transcript identifiers (MSTRG), what to do next depends on what you have already done!
If you haven’t run a merge step yet (predicted along with known to “merge”), then you can do that. If the predicted transcripts overlap with a known transcript, the annotation will be merged and the known label applied.
Some features might not merge into a known gene bound. Those are your predicted novel features.
You can generate your final counts to use for DE against the merged version of the annotation (novel + known) or you can just use the known. Maybe do both and compare?
Similar topics have this same advice. Search results for 'stringtie mstrg' - Galaxy Community Help
This tutorial goes through the process. → Hands-on: Reference-based RNA-Seq data analysis / Reference-based RNA-Seq data analysis / Transcriptomics
Hope this helps! 