12 April 2013

Bradyrhizobium and genome assembly

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System admin

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Seems like I’m a bit behind the times with MUMmer. Better options for multiple genome alignment include

But first, mapping-based assembly to B. japonicum genome using bowtie2.

Fairly easy to understand…got script running quickly!

#!/bin/bash -l
#PBS -l nodes=1:ppn=1,mem=24gb,walltime=6:00:00
#PBS -m abe

cd /home/tiffinp/stanton1/B-elkanii-genomes/bowtie2-assemblies

# Set variables

# Align contigs from velvet de novo assembly to Bradyrhizobium japonicum reference genome

# bowtie build
bowtie2-build $refgenome Bjaponicum

# bowtie assemble for each sample

for sample in IC1 ENC4 EWC3
        bowtie2 -x Bjaponicum -1 $read1 -2 $read2 --phred33 -S BT2-${sample}.sam --un ${sample}-unaligned

Spot-checked SAM output - looks good, but unaligned reads not being saved to separate file. Recommendation to remove unmapped reads using:

awk '$3!="*"' in.sam > in.filt.sam

Searches file for unmapped read with * in 3rd column. Can also do

awk '$3=="*"' in.sam > in.unaligned.sam

And remove original file.

Picard. Explain SAM flags


Meeting with NG.

  • transcriptome assembly/analysis
  • future experimental plans based on SHC meeting yesterday
    • why do we need to make composite colonies in lab?
    • JSG: control for maternal effects, development environment
    • how many colonies?


Useful git reminders from software carpentry git tutorial

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