Question: Allelic sequencing using NGS
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selma.maacha • 0 wrote:
Hello, I am trying to assess indels after CRISPR/Cas9 editing of a gene of interest. I extracted genomic DNA and amplified the locus of interest by PCR (350bp) then submitted the amplicon to NGS. I just got the FASTQ file for the submitted sample (text file with millions of reads, FASTQ format). I would like to compare these sequences to a reference sequence (350bp, Wild-type version of the locus) in order to assess the presence of indels and wether a given indel is present in both alleles (homozygous) or is heterozygous. Can you please recommend the steps I need to take in order to achieve that using Galaxy ? Thanks a lot for your help ! Best,