I performed normalize-by-median.py and the total number of reads reported does not match the actual total reads in the input file.
my script :
interleave-reads.py --gzip -o sample1_paired.fastq.gz sample1_R1.fastq.gz sample1_R2.fastq.gz
normalize-by-median.py --gzip -M 700G -R sample1_norm.report -o sample1_paired_norm.fastq.gz -p sample1_paired.fastq.gz
split-paired-reads.py --gzip sample1_paired_norm.fastq.gz -1 sample1_norm_R1.fastq.gz -2 sample1_norm_R2.fastq.gz
The report file for the normalization says: DONE with sample1_paired.fastq.gz; kept 272104114 of 310860582 or 87.5% so a total of 310860582 reads but the real total reads in sample1_paired.fastq.gz is 312 017 576 reads.
I have no idea where this difference comes from. Is it normal? What can cause it?
I performed normalize-by-median.py and the total number of reads reported does not match the actual total reads in the input file.
my script :
interleave-reads.py --gzip -o sample1_paired.fastq.gz sample1_R1.fastq.gz sample1_R2.fastq.gz
normalize-by-median.py --gzip -M 700G -R sample1_norm.report -o sample1_paired_norm.fastq.gz -p sample1_paired.fastq.gz
split-paired-reads.py --gzip sample1_paired_norm.fastq.gz -1 sample1_norm_R1.fastq.gz -2 sample1_norm_R2.fastq.gz
The report file for the normalization says:
DONE with sample1_paired.fastq.gz; kept 272104114 of 310860582 or 87.5%so a total of 310860582 reads but the real total reads in sample1_paired.fastq.gz is 312 017 576 reads.I have no idea where this difference comes from. Is it normal? What can cause it?