|
|
|
@ -37,9 +37,8 @@ git clone https://github.com/MillironX/cowcalf-rumen-metagenomic-pipeline.git
|
|
|
|
|
Create a directory with all forward- and reverse- read files in it, named as
|
|
|
|
|
`<SAMPLEID>_R1_001.fastq.gz` for forward-reads and `<SAMPLEID>_R2_001.fastq.gz`
|
|
|
|
|
for reverse-reads. Add a [QIIME2-compatible metadata file][qiime2-metadata]
|
|
|
|
|
named `metadata.tsv`, text files containing the minimum and maximum rarefaction
|
|
|
|
|
values names `rarefaction.min.txt` and `rarefaction.max.txt` and copy all of the
|
|
|
|
|
code files into it. It should look like
|
|
|
|
|
named `metadata.tsv`, and copy all of the code files into it. It should look
|
|
|
|
|
like
|
|
|
|
|
|
|
|
|
|
```plaintext
|
|
|
|
|
.
|
|
|
|
@ -51,8 +50,6 @@ code files into it. It should look like
|
|
|
|
|
├── sampleN_R1_001.fastq.gz
|
|
|
|
|
├── sampleN_R2_001.fastq.gz
|
|
|
|
|
├── metadata.tsv
|
|
|
|
|
├── rarefaction.min.txt
|
|
|
|
|
├── rarefaction.max.txt
|
|
|
|
|
├── main.sh
|
|
|
|
|
├── fastq-to-taxonomy.sh
|
|
|
|
|
├── manipulatefeaturetable.R
|
|
|
|
|