lower exon percentage

Question

[anubratadas]

Hi, i am new to RNA-seq analysis i aligned the RNA-seq from mouse tissue with STAR in pair end mode and STAR log file shows

                            - Number of input reads |   19657827
                       - Average input read length |    200                                         
                                 - UNIQUE READS:                       
                - Uniquely mapped reads number |    6255962
                       Uniquely mapped reads % |    31.82 %
                         Average mapped length |    194.88
                      Number of splices: Total |    2874161

for the same dataset, when i run RNA-seq analysis in qualimap as single end mode,

                               mapped reads | 51,353,872
                              alignements   | 69,290,152
                     secondary alignments   | 17,936,280
                     non-unique alignments  | 56,778,010
                        aligned to genes    | 10,358,920
                                intronic    | 13.18 %
                                exonic      | 83.74 %

when i run RNA-seq analysis in qualimap as pair end mode,

                  mapped reads (left/right) | 25,676,936/25,676,936
       aligned pairs (without duplicates)   | 25,676,936
                     secondary alignments   | 17,936,280
                     non-unique alignments  | 56,778,010
                        aligned to genes    |    366,114
                                intronic    | 60.67 %
                                exonic      | 31.93 %

i am not able to understand how the same dataset shows so much discrepancy ? Thanks Anubrata

[caggtaagtat]

So it seems like you have 2x 100nt long PE reads. Did you perform adapter trimming before aligning the reads? Adapter sequences at the end of the reads can reduce the number of mapped reads. What was the command you used for STAR aligning?

[anubratadas]

Hi, yes i did adapter trimming below is the STAR command:

STAR --runMode alignReads --runThreadN 40 --genomeDir mouse_genome_index --readFilesIn data/mouse-C_R1.fastq data/mouse-C_R2.fastq --outFileNamePrefix control --outSAMprimaryFlag AllBestScore --outReadsUnmapped Fastx --quantMode GeneCounts --twopassMode Basic