What is the meaning of ‘#nreads’ and ‘#avg_read_length’ at the end of the bowtie2 file?But “#nreads” is not the number of reads of the input file. For example:
Hi @song
Are the number of reads and their avg length of your input (of those that passed metaphlan quality controls). It is used internally by metaphlan when executing the profiling directly from the bowtie2out files
Thank you for your answer. But the number of reads in the actual input file is different from the bowtie2 file. Why does this happen? If possible, please test an example and check.