Transcript_id with "-0" after "flair collapse"

Question

[anna_shin]

Hi, I have some questions about flair output. I used the following scripts for generating isoform.gtf file.

FASTQ : Long-read RNA-Seq.fastq

BRAKER_GTF : gtf output file for braker program.

flair align -g ${REF} -r ${FASTQ} --output ${SAMPLE} --thread ${THREAD}

flair correct -q ../01_mapping/${SAMPLE}.bed -f ${BRAKER_GTF} -g ${REF} --output ${SAMPLE} --thread ${THREAD}

flair collapse -g ${REF} --gtf ${BRAKER_GTF} -q ../02_correct/${SAMPLE}_all_corrected.bed -r ${FASTQ} --stringent --check_splice --generate_map --annotation_reliant generate --output ${SAMPLE} --thread ${THREAD}

finally, I got isoforms.gtf file but there are some transcript ids with "-0" What are these transcripts that have '-0' in their names? Also, why are they named that way?

[cheong]

Hi anna, do you know the answer now?

Thanks.