I'm currently working on a mitochondrial long noncoding RNA,which is very special in term of its structure.

it's mitochondrial rRNA 16S with part of antisense 16S hanging on the 5' end.

I don't see any well accepted annotation file having this chimeric transcript included .

For I'm not familiar with the principle of alignment software using reference transcripts (e.g. salmon), whether it's error prone or not to quantify chimeric transcripts using this strategy. I think it's possible to get some information here?

• For validation, I tried to get some proof from nanopore sequencing data by checking if any reads spanning on the junction of the transcript, as its reads are long, but this didn't get me further.

• Chitars5.0 database doesn't have this record either.
• CCLE RNA-seq data was downloaded and analyzed using star and later star-fusion, but there is no luck. Below is the parameters I used for star pipeline

STAR --genomeDir /home/data/refdir/server/reference/index/star/hg38/ --readFilesIn /home/data/ssy042/CCLE/SRR8615717_1.fastq.gz /home/data/ssy042/CCLE/SRR8615717_2.fastq.gz --outReadsUnmapped None --twopassMode Basic --readFilesCommand "gunzip -c" --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30 --runThreadN 5


STAR-Fusion --no_annotation_filter --genome_lib_dir
/home/data/ssy042/ref/star_fusion/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ -J Chimeric.out.junction --output_dir SRR8615717.star