These are chat archives for dereneaton/ipyrad

11th
Jul 2016
Deren Eaton
@dereneaton
Jul 11 2016 17:56
Advanced tutorial has been updated.
v.0.3.20 is now up on conda for linux (Mac coming very soon):
  • Bug fix for variable length reads (e.g., GBS w/ overlap)
  • Speed improvements to step6
Robin Sleith
@R0cknRobin_twitter
Jul 11 2016 20:02
Hello, I am back at it, working through ipyrad with my data and have a quick question. The file we received from the sequencing facility came with a BLANK record in the .fastq file. When ipyrad demultiplexes and runs normally it gets stuck on step 4. When I delete the BLANK prior to running step 4 it works fine, until step 7, when it fails because BLANK The following Samples do not appear to have been clustered in step6. In a previous version there was a setting to exclude a sample for step 7. It appears to not be there in the latest release. It would be nice to be able to exclude from the very beginning so that I do not have to stop and start the process to delete BLANK.fastq after step 2. Thank you much! Robin
Deren Eaton
@dereneaton
Jul 11 2016 20:25
Hi @R0cknRobin_twitter, yes you can 'delete' a sample by branching such that you keep all of the other samples in your data set besides the one you wish to exclude:
## the format to branch and subsample is:
ipyrad -p {params-file} -b {new-branch-name} {sample-names-to-keep-or-filename-with-sample-names} 

## example of listing sample names after the new assembly name
ipyrad -p params-data1.txt -b data2 sampleA sampleB sampleC

## example of using a file with sample names after the assembly name
ipyrad -p params-data1.txt -b data2 subsample.txt

## Example subsampling file: subsample.txt
sampleA
sampleB
sampleC
You could do this at any step, so excluding BLANK before step6 should fix your problem.