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A pipeline for processing MIRNA data
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README.md
SEQEM
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mirna_pipe.py

README.md

mirnapy

Author: Gene Blanchard

Email: me@geneblanchard.com

Requirements

  • fastx_toolkit
  • bwa

If using ubuntu you can install with sudo apt-get install bwa fastx-toolkit, you may also need to install libgtextutils.

If using mac I recomend recomend to install homebrew. Next install the homebrew-science repo with brew tap homebrew/science. Install the fastx-toolkit and bwa with brew install bwa fastx_toolkit

Example

mirna_pipe.py -i A1.fastq,B1.fastq,A2.fastq,B2.fastq -o A1_B1_A2_B2_output
This would create the A1_B1_A2_B2_output folder in your current working directory.

Database

The default database is located at DB_mature/mouse/mature_dna_mouse.fa change this with the -d option

Output

The output contains the folowing:

  • commands.txt
  • A file that lists all commands run
  • clipped_files/
  • The output of the fastx clipping
  • alignment_files/
  • The output of the BWA alignment
  • SEQEM/
  • The results of the SEQEM command
  • counts/
  • Raw counts from the SEQEM command
  • RSEM/
  • Groomed tab-seperated files that are ready to input into RSEM

TODO

Need to add sequence length filtering options

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