I have a FASTQ file (name as Origin_ELW24.fastq.gz) with 107,856,041 single-end 75bp reads. After trimming and alignment, we get a BAM file (name as ELW24.bam) via STAR. I use commands below to convert the BMA file to a new FASTQ file (name as New_ELW24.fastq.gz). The number of reads in the new FASTQ file is 122,444,250 that more than the number of reads in the original FASTQ file. I don't understand why the number of reads will increase after the trimming and alignment. Could you help me? Many thanks.
bedtools bamtofastq -i ELW24.bam -fq New_ELW24.fastq
gzip -c New_ELW24.fastq > New_ELW24.fastq.gz