Bowtie2

System admin

Information for:

Bradyrhizobium

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
refgenome=Bjaponicum_USDA110_ref_genome.fasta
read1="/home/tiffinp/stanton1/B-elkanii-genomes/fastq-quality-trimmed/IC1_R1_seqtk_trimmed_clipped_stillpaired.fastq"
read2="/home/tiffinp/stanton1/B-elkanii-genomes/fastq-quality-trimmed/IC1_R2_seqtk_trimmed_clipped_stillpaired.fastq"

# 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
do
        bowtie2 -x Bjaponicum -1 $read1 -2 $read2 --phred33 -S BT2-${sample}.sam --un ${sample}-unaligned
done

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

Aphaenogaster

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?

Computing

Useful git reminders from software carpentry git tutorial