To-do list- data cleaning step

[gauravsk]

Data cleaning

• check if user has periods in file names; break script if so and ask user to rename files
• rewrite the perl script into python; make it put all of the cleaned output files into a new folder

[limey-bean]

that would be rad!

[gauravsk]

This may help with converting check_paired.pl to python: https://github.com/enormandeau/Scripts/blob/master/fastqCombinePairedEnd.py

[limey-bean]

I like it, the only issue is that it makes a single unpaired reads file. Would it be hard to make two unpaired reads files (F and R)?

[gauravsk]

Oh, yeah, didn't mean to suggest that as a final version, more a note to self for me to look at how this script does it when I write one to our needs.

[limey-bean]

Cool cool, It is a good template.

[gauravsk]

• The QC folder is emptied out by the end of the full run-- need to figure out where, exactly, and maybe also remove the directory itself (right now the directory is kept, but it is empty). Alternatively, maybe add an option to allow users to retain the QC'd stuff if they want to keep it.

[gauravsk]

• Get rid of the line that generates the error QC/cutadapt_fastq/primer_sort/*_*_Paired_1.fastq not found in every run