output files from the zcat pipe command

[Ming Liao]

Hello, there

I tried the demo here http://huttenhower.sph.harvard.edu/kneaddata, I can get the output the same as the manual said  (There were only 2 fastq files):

The examples folder contains a demo input file. This file is a single read, fastq format.

$ kneaddata --input examples/demo.fastq --reference-db examples/demo_db --output kneaddata_demo_output

This will create four output files:

1. kneaddata_demo_output/demo_kneaddata.fastq
2. kneaddata_demo_output/demo_kneaddata_demo_db_contam.fastq
3. kneaddata_demo_output/demo_kneaddata.log
4. kneaddata_demo_output/demo_kneaddata.trimmed.log

But when I tested the "zact" in a pipe command, what I got were the following four files: (There were 3 fastq files now!)

$ kneaddata --input examples/demo.fastq.gz --reference-db examples/demo_db --output kneaddata_demo_output

This will create four output files:

1. demo_kneaddata.fastq
2. demo_kneaddata_Homo_sapiens_bowtie2_contam.fastq
   
3. demo_kneaddata.log
4. demo_kneaddata.trimmed.fastq
   

Is the first one demo_kneaddata.fastq the original raw data just unzipped from demo.fastq.gz?   

The last one demo_kneaddata.trimmed.fastq was the trimmed fastq that is clean so that it can be applied to metaphlan2? 

Thanks

Ming 

[Andy Shi]

Hi Ming,

It seems like the documentation on our website might be a bit stale.

The file that you want is demo_kneaddata.fastq, which contains the cleaned reads.