How can i extract specific genes from WGS sequence.
I have 48 rice whole-genome sequences and I would like to extract tolerant genes among them. I already make assemble with MSUv6.1 (all.con) from (http://rice.plantbiology.msu.edu/) and I have sorted.bam file. So now to extract tolerant gene what should I need to do further? If any expert suggested me some workflow for further steps it would be much appreciated. Thank you in advanced
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Since you have aligned (not assembled) your data against a reference you must know the genomic coordinates of genes you are interested in. You can subset your BAM files to generate smaller BAM files for those regions using
samtools viewwith relevant intervals e.g. "Chr10:18000-45500". Once you have the smaller BAM files you can generate consensus sequences for each by using the directions here: Generating consensus sequence from bam fileThanks for your suggestion. I will work on it