28 March 2013

aphaenogaster, simulations, and transcriptomics

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RNAseq simulation

Research

Generate simulated data for RNAseq analysis pipeline. Couldn’t get DWGSIM to install correctly so used wgsim from SAMTools

Options allow sequencing error, mutation rate, and variation in read length.

Usage:   wgsim [options] <in.ref.fa> <out.read1.fq> <out.read2.fq>

• Typical Illumina error rates ~1.3% forward and 1.7% reverse according to SEQanswers

Test by simulating 1,000 2x100PE RNAseq with 500bp size selected fragments, no mutations. created test input data file by copying first ~6 contigs from Pogonomyrmex barbatus predicted transcriptome

./wgsim -d 500 -s 50 -N 1000 -1 100 -2 200 -r 0 -R 0 Pbar_transcriptome_test.fa out.read1.fq out.read2.fq

Worked perfectly! Generated 978 reads. fastq sequence identified specifies the contig that each read came from. number of reads per contig ranged from 85 to 241. note that contigs less 650 bp in length disregarded.

Helms-Cahan Lab group

Jai practice talk for EcoLunch