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Pull FASTQ reads and map them with a gene

Hello,

I want to pull fastq reads those who are mapping with a gene. After that, also need to find out the coverage and depth of the reads those who are mapped/aligned with the gene.

How to carry on the work ?

Please share your research ideas/bioinformatics technqiues for the above problem.

thanks, in-advance.

snp next-gen sequencing fastq genome

samtools view input.bam "Chr10:100-200" > output.bam

This will extract the reads from bam file that are in the region 100:200 in chr10 as example (make sure to know how your chromosomes are named). But this is the reads only (not fastq) from the reads name you can write script or maybe there is already some tools to do that extract there corresponding fastq reads

a lot of examples for this issue already exist here

The answer for the coverage section is here A: Depth of coverage for specific target from bam file

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