I have data generated from illumina Miseq 1.9 for 24 samples, which are paired ends (300X2). The instrument reads a 500-600 read fragment and run a paired end protocol. Looking at Fastq files multiqc report, I realized that R1 and R2 of samples have a length of 175-260 bp (See 1) , not even 300 bp. I do know how sequencing work, and I am only surprised from those samples lying below 200 for instance ! by looming at the Fastqc report, those samples with small average read length (175 or 200) have humbs around the middle (in the sequence length distribution (See 2) I also observed that those reads with the shorterst length have more abundance (higher seq. depth) and also better phred score quality. Can one trust these runs ? Any comments ?
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