How to extract a sequence of specific gene from my own genome

Question

[Aj15]

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.

Cheers,

[Ankit]

Which data is this? Follow the analysis pipeline according to data. There are several tools available.

[Aj15]

I edited the post, Ill look into the analysis pipeline for the data.

Thank you.