Skip to content
This repository has been archived by the owner on Nov 9, 2023. It is now read-only.

split_libraries.py -- issue #2211

Open
shrutidabral opened this issue Feb 15, 2018 · 0 comments
Open

split_libraries.py -- issue #2211

shrutidabral opened this issue Feb 15, 2018 · 0 comments

Comments

@shrutidabral
Copy link

hi,
I m using QIIME for OTU identification.
I have raw paired fastq files.

i do not have any information of barcode and linker primer .So i decided to create a barcode file using extract_barcodes.py script. this command run sucessfully and as a result i got three files read1.fastq resd2.fastq and barcodes.fastq.

command i used is --
extract_barcodes.py --input_type barcode_paired_end -f CIM_R1.fastq -r CIM_R2.fastq --bc1_len 6 --bc2_len 8 -o parsed_barcodes/

my query is ---

  1. what is meaning of this --bc1_len 6 and --bc2_len 8 ? Its seems to be a length of barcode but how can i decide this is perfect lenght for my raw data.
  2. Now, how can i use these file in split_libraries.py script. i read the tutorial but i am not able to understand.
  3. can we run the whole process without having information of barcode and linkerprimer.?
Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant