diff --git a/doc/11.experiment-challenge.md b/doc/11.experiment-challenge.md index 71de583..9f2523d 100644 --- a/doc/11.experiment-challenge.md +++ b/doc/11.experiment-challenge.md @@ -21,13 +21,13 @@ cd ~/2020-NSURP/raw_data Download the files ``` -wget https://ibdmdb.org/tunnel/static/HMP2/WGS/1818/HSMA33S4.tar -wget https://ibdmdb.org/tunnel/static/HMP2/WGS/1818/HSMA33R1.tar -wget https://ibdmdb.org/tunnel/static/HMP2/WGS/1818/HSMA33R5.tar +wget https://ibdmdb.org/downloads/raw/HMP2/MGX/2018-05-04/CSM7KOJO.tar +wget https://ibdmdb.org/downloads/raw/HMP2/MGX/2018-05-04/HSMA33R1.tar +wget https://ibdmdb.org/downloads/raw/HMP2/MGX/2018-05-04/HSMA33R5.tar -wget https://ibdmdb.org/tunnel/static/HMP2/WGS/1818/MSM6J2QP.tar -wget https://ibdmdb.org/tunnel/static/HMP2/WGS/1818/MSM6J2QF.tar -wget https://ibdmdb.org/tunnel/static/HMP2/WGS/1818/MSM6J2QH.tar +wget https://ibdmdb.org/downloads/raw/HMP2/MGX/2018-05-04/MSM6J2QP.tar +wget https://ibdmdb.org/downloads/raw/HMP2/MGX/2018-05-04/MSM6J2QF.tar +wget https://ibdmdb.org/downloads/raw/HMP2/MGX/2018-05-04/MSM6J2QH.tar ``` Untar each read set @@ -71,9 +71,9 @@ mkdir -p ~/2020-NSURP/metadata cd ~/2020-NSURP/metadata ``` -All information about this project can be found [here](https://ibdmdb.org/tunnel/public/summary.htmlhttps://ibdmdb.org/tunnel/public/summary.html). +All information about this project can be found [here](https://ibdmdb.org/). -Download the metadata file [here](https://ibdmdb.org/tunnel/products/HMP2/Metadata/hmp2_metadata.csv). +Download the metadata file [here](https://ibdmdb.org/downloads/metadata/hmp2_metadata_2018-08-20.csv). This file contains information for the metagenomics sequencing (which we looked at), but also a number of other assessments. @@ -81,24 +81,24 @@ This file is a spreadsheet that can be opened in Google docs or viewed with `les For example, view this file with less like so: ``` -less -S hmp2_metadata.csv +less -S hmp2_metadata_2018-08-20.csv ``` This is a very large file. You can get information about a specific sample by searching out the specific sample id's we used. For example: ``` -grep HSMA33S4 hmp2_metadata.csv +grep HSMA33S4 hmp2_metadata_2018-08-20.csv ``` That's still a lot of info - let's get only the info for metagenomics samples: ``` -grep metagenomics hmp2_metadata.csv | grep HSMA33S4 +grep metagenomics hmp2_metadata_2018-08-20.csv | grep HSMA33S4 ``` The formatting is still a litle ugly. Let's direct the output to a file, and then open it with `less -S`: ``` -grep metagenomics hmp2_metadata.csv | grep HSMA33S4 > HSMA33S4.csv +grep metagenomics hmp2_metadata_2018-08-20.csv | grep HSMA33S4 > HSMA33S4.csv less -S HSMA33S4.csv ```