STARsolo intergenic reads as same as antisense #1733
Description
Hello developer:
I use STARsolo to analyze SPLit-seq data. My command is:
STAR \
--runMode alignReads \
--soloCellFilter EmptyDrops_CR \
--runThreadN 16 \
--genomeDir ${star_index} \
--readFilesIn ${R1_fq} ${R2_fq} \
--readFilesCommand zcat \
--outSAMattributes NH HI nM AS CR UR CB UB GX GN sS sQ sM \
--outSAMtype BAM SortedByCoordinate \
--soloCBwhitelist ${barcode_list1} ${barcode_list2} ${barcode_list3} \
--soloType CB_UMI_Complex \
--soloCBposition 0_10_0_17 0_48_0_55 0_86_0_93 \
--soloUMIposition 0_0_0_9 \
--soloCBmatchWLtype EditDist_2 \
--soloFeatures GeneFull_Ex50pAS \
--soloMultiMappers EM \
--soloCellReadStats Standard \
--outSAMunmapped WithinI use --soloFeatures GeneFull_Ex50pAS, and use the output file Solo.out/GeneFull_Ex50pAS/CellReads.stats to calculate the ratio of intergenic regions and antisense genes.However I got exactly the same reads. I calculated it like this：
intergenic = genomeU + genomeM - exonic - intronic
antisense = exonicAS + intronicASIs it because the reads aligned to non-introns and non-exons are classified as antisense?
Thank you!