Creosote

Creosote genome sequencing and assembly notes:

• Sample obtained from front yard of 4951 W. McElroy Dr.
• Sequences obtained from one lane of Illumina HiSeq2000
• Fastq files delivered from UAGC
  • 82 files
    • lane3_NoIndex_L003_R1_041.fastq
    • lane3_NoIndex_L003_R2_041.fastq
  • Need to understand if these are paired-end reads
  • Need to get adapter sequences used in sequencing
  • Description of Fastq file format with notes on specific decoding of header names generated by various technologies: http://en.wikipedia.org/wiki/FASTQ_format
• Check quality with fastqc: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
  • Creosote First Run FastQC

• Sequences cleaned using trimReads by Haibao Tang: https://github.com/tanghaibao/trimReads/tree/
  • NOte: Only use on single reads
  • Ran with supplied adapter sequence file:

>Adapter 4
TGACCA
>Adapter 4 rc
TGGTCA

• • Command-line run:

Running /home/elyons/bin/trimReads  -Q 33 -f /home/elyons/projects/genome/data/creosote/Sample_lane3/adapter/adapter.faa ./lane3_NoIndex_L003_R2_015.fastq

• • Output of trimReads:

• Trim Paired ends with Trimmomatic: http://www.usadellab.org/cms/index.php?page=trimmomatic
• Assumes Illumina Encoding (code: 64, not code: 33)
  • Need to convert for the HighSeq Reads:
  • easy_install biopython
  • git clone git://github.com/tanghaibao/jcvi.git
  • export PYTHONPATH=/lib/python (which is the dir above jcvi)
  • python -m jcvi.formats.fastq (Install missing packages)

Steps:

• Merge R1 files; merge R2 files
• gzip them
• Run this: python -m jcvi.apps.baseclean trim R1.fastq.gz R2.fastq.gz
  • NOTE: This program should download trimmomatic, but may need to update the path of the timmomatic program in the program
• Note: Bao recommends CLC for genome assembly. Runs faster, less memory, less sensitive to bad data. Compute intensive.

• python -m jcvi.formats.fastq convert (read help file, default converstion
• python -m jcvi.apps.baseclean trim fastqfile (single ended)
• python -m jcvi.apps.baseclean trim R1.fastq.gz R2.fastq.gz (paired ended)

• Cat all the R1s together
• Cat all the R2s together