Add samples from SRP018247

[k8hertweck]

• update SRP018247.lst

• uncomment lines 16-19 in mothur_prep.sh

• update line 39 in mothur_prep.sh

• update line 45 in mothur_prep.sh

• update line 48 in mothur_prep.sh

• run mothur_prep.sh to test

• checking parameters in mothur_otu.bat

[aortiz24]

I have updated SRP018247.lst and uncommented lines 16-19 in my new branch called "New_samples".

I am unclear as to the updates I need to make to line 39, 45, and 48 in mothur_prep.sh. Clarification is needed and appreciated.

I ran dataDownload.sh before I tried to run mothur_prep.sh. I ran into a problem:
fastq-dump: command not found, I think this error is popping up because SRATool kit is not installed on the mac mini.

[k8hertweck]

Great!

Regarding lines 39, 45, and 48: these lines execute the mothur commands to prep the combined/merged files. You need to add the extra samples from SRP018247.

Do you still have the original fastq file downloads? You can manually move them to the data folder. Otherwise, let me know and I'll email you the links to redownload from my Dropbox. I'll also install the software on the mac mini.

[k8hertweck]

Could you please check and make sure SRP018247.lst matches the files Katrin wanted included in this analysis? If you go to the data overview spreadsheet in Google Drive, the "design" spreadsheet includes which samples she wanted excluded; these should be removed from the list of samples.

[aortiz24]

I have completed the top five tasks this issue #13 and have launched a PR.

[aortiz24]

I have ran mothur_prep.sh to test the analysis and it is running smoothly(6th task on issue #13). I double checked that the samples highlighted in the dataoverview doc were excluded. With your approval, we could be ready to run the mothur_prep.sh for SRP018246 and SRP18247!

[k8hertweck]

I think there were a few samples assigned incorrectly, but they should be good to go now. I'm merging and doing a test run; could you double check?

[k8hertweck]

Last checkbox here resolved by #30