Remapping your reads to your assembled transcriptomeΒΆ

First, we’ll need to make sure bowtie2 is installed:

sudo apt-get install -y bowtie2

Now, create a bowtie2 index out of your transcriptome:

cd /mnt/work
gunzip -c trinity-nematostella-raw.renamed.fasta.gz > trinity-nematostella-raw.renamed.fasta
bowtie2-build  trinity-nematostella-raw.renamed.fasta transcriptome

And then, finally, count the number of reads that map to your transcriptome:

zcat 0Hour_ATCACG_L002_R1_001.extract.fastq.gz | \
     head -400000 | \
     bowtie2 -U - -x transcriptome > /dev/null

You should get something like:

97.18% overall alignment rate

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