Hello,
I am working with PE 150bp Illumina HiSeq X-ten sequencing data.
I have generated the number of reads in my trimmed forward + reserve paired fastq files using FASTQC, by counting the number of lines with zcat and by looking at Trimmomatic results. The counts of the number of reads are concordant.
Then, I have mapped the forward+reverse paired reads to the reference genome using bwa-mem and run bamtools on the output to get the total number of reads and the number of mapped reads. Both the total number of reads and the number of mapped reads are higher than the number of reads in the fastq files (reverse+forward).
Could it be because the mapped reads can have more than one alignment and the total number of reads does not correspond to the input number of reads but the number of mapped reads which may have multiple alignment + the number of unmapped reads?
Thanks,
Marie
I am working with PE 150bp Illumina HiSeq X-ten sequencing data.
I have generated the number of reads in my trimmed forward + reserve paired fastq files using FASTQC, by counting the number of lines with zcat and by looking at Trimmomatic results. The counts of the number of reads are concordant.
Then, I have mapped the forward+reverse paired reads to the reference genome using bwa-mem and run bamtools on the output to get the total number of reads and the number of mapped reads. Both the total number of reads and the number of mapped reads are higher than the number of reads in the fastq files (reverse+forward).
Could it be because the mapped reads can have more than one alignment and the total number of reads does not correspond to the input number of reads but the number of mapped reads which may have multiple alignment + the number of unmapped reads?
Thanks,
Marie
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