Step 1/Trimmomatic issues with matching up paired-read files

[Jordyn Broadbent]

Hi there, 

I am currently running the master script, and the script/syntax for Step 1 as written is resulting in odd pairing of read files in Trimmomatic. I have ensured that the naming convention for input read files follow what is included in the sample_files_paired ends. Specifically, it only processes _R2 (SE) for the first three samples within my input folder, then runs PE (correctly) on all other paired read files. I have four different input folders where this has occurred -- again, with no tweaking of the master script.

I have tried tweaking the script myself to remove SE as an option and more accurately pair up _R1/_R2 files, however am not having much luck. 

Mostly curious if this has been noted for anyone else/before?

Please let me know if I can provide any further information, 

JB

[Sam Westreich]

Hey Jordyn,

Could you share the names of the files in your input folder?  You could run "ls" on the folder and just copy-paste the results into an email back, perhaps; I want to see if I spot anything.  I don't know why it would fail on the first 3 but work on the others, since the loop is per-file, but I can try and diagnose.

Best,

Sam

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Sam Westreich, PMP, PhD

Microbiome Scientist, DNAnexus, 

http://www.mosaicbiome.com