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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