These are chat archives for dereneaton/ipyrad

25th
Sep 2016
R2C2.lab
@R2C2_Lab_twitter
Sep 25 2016 14:38
R2C2.lab
@R2C2_Lab_twitter
Sep 25 2016 14:51
ipyrad.tiff
@edgardomortiz the path is specified in parameter [4] (check above) and sequences are named as MC-O1_R1.fastq.gz and MC-O1_R2.fastq.gz , so I suppose must be something else. This is what I get when executing the first option
Edgardo M. Ortiz
@edgardomortiz
Sep 25 2016 14:58
Your sequences must be named MC-O1_R1_.fastq.gz and MC-O1_R2_.fastq.gz, respectively, the second underscore is missing.
You can rename them easily with two loops:
for file in *_R1.fastq.gz; do mv $file ${file//_R1/_R1_}; done
for file in *_R2.fastq.gz; do mv $file ${file//_R2/_R2_}; done
R2C2.lab
@R2C2_Lab_twitter
Sep 25 2016 15:06
@edgardomortiz sorry, I just understand the other way around! I thought that they couldn’t have underscores. It seems to be working now. Many thanks!!!
ipyrad2.tiff
Edgardo M. Ortiz
@edgardomortiz
Sep 25 2016 15:07
Great!
R2C2.lab
@R2C2_Lab_twitter
Sep 25 2016 15:25
ipyrad.tiff
@edgardomortiz false alarm :-( apparently is not saving anything in the pooled_fastqs output directory
But probably it was not supposed to save anything there because the sampes are already demultiplexed and it’s actually doing something in step 2
ipyrad2.tiff
many thanks @edgardomortiz you saved my day!
Edgardo M. Ortiz
@edgardomortiz
Sep 25 2016 15:32
Yes, I am putting my demultiplexed files in a folder with the same name of my analysis followed by _fastqs to follow ipyrad naming conventions, the results of step 2 go to the folder ending in _edits
R2C2.lab
@R2C2_Lab_twitter
Sep 25 2016 15:45
@edgardomortiz step 2 finished and step 3 already running!
Edgardo M. Ortiz
@edgardomortiz
Sep 25 2016 15:55
Excellent, glad to help