Demux and visualization of data

[ben (benjamin w.)]

Yes, put them into one line.

Also, all the of -- were converted into the long dash -. Ben

[HebaHussein-1981 (Heba Hussein)]

I got a message to add (f) to the trim and I tried adding f and still getting error. how we can make the trim zero to make it easier?
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-trim-left-f-6 --p-trim-right-f --p-trunc-len-f 225 --p-trunc-len-r 218 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising_stats.qza

(1/2?) no such option: --p-trim-left-f-6 (Possible options: --p-trim-left-f,

--p-trim-left-r)

(2/2?) no such option: --p-trim-right-f

[ben (benjamin w.)]

qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-trim-left-f 6 --p-trim-left-r 7 --p-trunc-len-f 225 --p-trunc-len-r 218 --p-n-threads 0 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising_stats.qza

--p-trim-left-f-6 (in case you wanted to identify the issue, there was a dash that connected your modifier "--p-trim-left-f" to "-6" and qiime didn't like it!

Not sure why your code has dashes all over the place, but that's ok. Try running that above. Ben

[HebaHussein-1981 (Heba Hussein)]

thanks it seems running but it seems will take long time. although I am using only 6 sample. one tutorial i watched said it took 4 days. also, I got a message that the path incorrect so I entered the aboslute path although in all tutorials they use relative path

[ben (benjamin w.)]

Depends on how complex the samples are (richness/diversity). If they are stool, it may take a while, but I would recommend running it on a beefy computer (+ a lot of RAM / decent processor). Ben

[HebaHussein-1981 (Heba Hussein)]

thanks it run but cant find the files on desktop as usual and when I searched on mac, cant reach them. also, visualization of these three file using the same website as we did before?!

edit: I will try to summarize it as I did for the visualization to see it
DADA2|690x61

[ben (benjamin w.)]

@ben

qiime dada2 denoise-paired --i-demultiplexed-seqs /Users/hebahussein/Desktop/paired-end-demux.qza --p-trim-left-f 6 --p-trim-left-r 7 --p-trunc-len-f 225 --p-trunc-len-r 218 --p-n-threads 0 --o-table /Users/hebahussein/Desktop/table.qza --o-representative-sequences /Users/hebahussein/Desktop/rep-seqs.qza --o-denoising-stats /Users/hebahussein/Desktop/denoising_stats.qza

You should output your files to a place where you know you can find them, such as a desktop fold. Ben

[thermokarst]

Yep, this is great advice! Just to follow up though, @HebaHussein-1981, your files were output to your Home Directory, you can find them there for now.