Discrepancy between total numbers of seqs in fastq data and number of input reads in STAR program
Recently I used STAR program performed alignment for a paired-end RNASeq data and noticed a significant discrepancy between reads numbers. For example, the number of sequences from one sample is 71,346,020*2 (R1+R2)= 142,692,040. However when I check the number of input reads in STAR program, the number is 46,976,020 which is about 1/3 of the raw sequences. Does somebody have some explanation?
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It could be due to several reasons, I guess. Could you please post your STAR command here?