I have paired-end RNA-seq data aligned by STAR, I used featuresCount in order to get read summarization.(I know that STAR can give the count, but I would like to try with featuresCount). I don't understand why if I use the "-s 2" option I obtained a lower number of assigned read than without it.
This is the output of STAR:
Mapping speed, Million of reads per hour | 66.37 Number of input reads | 20999464 Average input read length | 202 UNIQUE READS: Uniquely mapped reads number | 18063283 Uniquely mapped reads % | 86.02% Average mapped length | 200.30 Number of splices: Total | 4054756 Number of splices: Annotated (sjdb) | 0 Number of splices: GT/AG | 4012566 Number of splices: GC/AG | 28175 Number of splices: AT/AC | 1578 Number of splices: Non-canonical | 12437 Mismatch rate per base, % | 0.31% Deletion rate per base | 0.02% Deletion average length | 1.36 Insertion rate per base | 0.01% Insertion average length | 1.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1876550 % of reads mapped to multiple loci | 8.94% Number of reads mapped to too many loci | 40430 % of reads mapped to too many loci | 0.19% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.79% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%
This is the output of featuresCount with the following command:
featureCounts-T 5 -t exon -g gene_name -a /Homo_sapiens.GRCh38.89.chr.gtf -s 2 -o output align.bam
Assigned 8798522 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_Chimera 0 Unassigned_FragmentLength 0 Unassigned_Duplicate 0 Unassigned_MultiMapping 11493680 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_NoFeatures 26603481 Unassigned_Overlapping_Length 0 Unassigned_Ambiguity 724563
And this is the output without using the -s 2 option:
Assigned 16492987 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_Chimera 0 Unassigned_FragmentLength 0 Unassigned_Duplicate 0 Unassigned_MultiMapping 11493680 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_NoFeatures 17636623 Unassigned_Overlapping_Length 0 Unassigned_Ambiguity 1996956
Thank you in advance!