Extracting the mapped sequence of a certain gene

Question

[randy.kang]

Hello, guys.

First, I feel embarrassed to ask this seemingly fundamental question for all of you and I am very unfamiliar with FASTQ/BAM handling..... Recently, we are trying to design a probe for RNA scope (or maybe possibly antibody as well in the future) that we found in the scRNA sequencing study recently. Is there anyway that we extract the sequence of the gene (probably partial or intron-region genes) which was recognized as our gene of interest?

Thanks a tone in advance guys!!

Answer 1

[Shred]

Easy:

samtools view -L your_gene.bed your_alignment.bam

Where your_gene.bed is the coordinates of your gene as a BED and your_alignment.bam contains aligned sequences.

[randy.kang]

Thank you so much!!!!