How to extract a sequence of specific gene from my own genome
Hello everybody, I’m new to bioinformatics and would like to extract a sequence from mapped reads.
I start off with 2 read files that are rna-seq data of a sequenced individual and a reference transcriptome from ncbi.
1) Use Fastqc to Quality control the 2 read files
2) use bowtie2 to map the read files to reference transcriptome
3) Assemble the mapped reads using an assembler ( Don’t know any, I’ll google and find some)
4) Use ncbi to find my gene of intreats and align the sequence with assembled transcriptome using symap (How to use a genome assembly file to extract or find the gene or region I am interested in?)
5) Extract the region that was aligned.
Is my strategy correct? Im unsure of steps 4 and 5.
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