Is it necessary to run trimmomatic before HUMAnN? My read number decreased from around 10000000 to 7000000 in forward read and 2000000 in reverse read

[lauren.j.mciver]

Hi, No worries! Sorry again for this inconvenience. We will get the use cases of 1) missing pair ids and 2) space additions in sequence ids covered in the next version of kneaddata.

For now use the following command to remove any spaces.

$  sed 's/ //g' < original.fastq > new.fastq

Thanks,
Lauren