Hello everyone,
I am working on a project aimed at reconstructing the transcriptome to discover new tissue-specific transcripts in the mouse. I have two replicates for each group: a WT_tissueX group and a Mutant_tissueX group. Below is a brief description of my transcript assembly method.
Transcript Reconstruction with StringTie:
stringtie -p 8 -c 5 -j 5 --rf "$BAM_FILE" -G $GTF_FILE -o "$OUTPUT_GTF"
Transcript Assembly with TACO:
`taco_run -p 8 pathGtf_Mutant_tissueX -o $OUT_DIR/taco_WT_tissueX taco_run -p 8 pathGtf_Mutant_tissueX -o $OUT_DIR/taco_Mutant_tissueX`
Merging Assembly Files with StringTie:
stringtie --merge -G $GTF_FILE -o $OUT_DIR/assembly_taco_merged.gtf $INPUT_DIR/assembly*.gtf
In the figure above, I do not understand where the exons highlighted in red come from, as there are no reads aligned in this region.
Hi,
You could first click on the highlighted tracks to expand them. Hovering your mouse over the exons will show you also more information. With that you can check the log-file of your first stringtie / taco run. Checking which tool included these exons.
Using your location information, you can also extract the output from your GTF for the specific gene (e.g. bedtools intersect ).