Clustering the transcriptomes

I have now made eight transcriptomes. Four from the resistant plants and four from the susceptible. To be able to compare expression from different times, and between the different biological replicates, I have to make a single transcriptome for the plant species, in this case, Syzygium (Lilly Pilly). This is a bit concerning as my plants are grown from wild sourced seeds and are likely to be highly heterozygous.

My approach therefore was to use the CD-HIT-EST-2D (http://weizhongli-lab.org/cd-hit/) software to combine transcriptomes, initially at 0.95  similarity. I clustered the transcriptomes in pairs from the largest to the smallest until I had a single fasta file.

#PBS -P (project)
#PBS -N SYZ1_CD-HIT
#PBS -l nodes=1:ppn=20
#PBS -l walltime=00:15:00
#PBS -l pmem=24gb
#PBS -e ./SYZ1.error
#PBS -M (email address)
#PBS -m abe

# Load modules
module load cd-hit/4.6.1

# Working directory
Input path to directory

# Run CD-Hit script
cd-hit-est-2d -i BU.fasta -i2 BS.fasta -o SYZ1.fasta -c 0.95 -n 10 -d 0 -M 0 -T 0

I then sought out highly conserved genes using local BLAST in BioEdit. I used a couple of Eucalyptus grandis chitinase genes that I know to be well conserved from previous work, currently under review.

I found that the genes were present and intact in the individual transcriptomes but not in the combined one. I therefore ran the process with CD-HIT again with a higher stringency of 0.98.

This time the genes were present in the final transcriptome making me feel more confident about the alignment process.

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