Entering edit mode
9 days ago
anna_shin
•
0
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?
