Larvae Example Workflow- M1 Data (Spermatozoa from Male 1)

This is an example of my workflow for my bisulfite sequencing larvae dataset. I am working with a total of 28 files and will narrow it down to a workflow of 7 datasets (1 female/eggs, 2 males/sperm, and 4 larvae samples)

1. Upload raw data to iPlant and unzip/uncompress this file this file using the gunzip analysis application

_87__Discovery_Environment_18C6A781.png
_87__Discovery_Environment_18C6A7B0.png

2. Dowload uncompressed files and relocate to Eagle

File locations for M1 uncompressed (Nov): http://eagle.fish.washington.edu/Mollusk/index.php?dir=bs_larvae_exp%2FUncompressed_Nov%2F

Directory_Listing_of__Mollusk_bs_larvae_exp_Uncompressed_Nov_18C6A8BC.png

3. Concatenate November and September uncompressed files (R1 and R2 separate). These are technical replicates from the Bisulfite sequencing run.

M1_R1

In []: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq

M1_R2

In []: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq

Location of concatenated files:

R1: http://eagle.fish.washington.edu/Mollusk/index.php?dir=bs_larvae_exp%2FConcatenated_Files_R1%2F

R2: http://eagle.fish.washington.edu/Mollusk/index.php?dir=bs_larvae_exp%2FConcatenated_Files_R2%2F

4. Upload these files to iPlant using the "Import from URL" function. This allows me to import multiple files from the URL location on Eagle.

_87__Discovery_Environment_18C6AB07.png

5. Run BSMAP in iPlant

_87__Discovery_Environment_18C6AD33.png
_87__Discovery_Environment_18C6AD66.png
_87__Discovery_Environment_18C6AD66.png
_93__Discovery_Environment_18C7E400.png

6. Download BSMAP files from iPlant and upload to Eagle

In []: 
ir="/usr/local/bin/irods3.2.icmds.mac.intel/"
In []: 
!{ir}/icd Larvae
In []: 
!icd /iplant/home/che625/Larvae/BSMAP
In []: 
!iget /iplant/home/che625/Larvae/BSMAP/BSMAP_analysis_M1-2014-03-04-17-56-24.707/logs/condor-stdout-M1 /Volumes/web-1/Mollusk/bs_larvae_exp/BSMAP_output

7. Run methratio in iPython

In []: