Question: CRISPR/Cas9 and allelic NGS to assess indels homozygocy or heterozygocy
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gravatar for selma.maacha
2.3 years ago by
selma.maacha0 wrote:

Hi everyone, 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 anyone recommend the steps I need to take in order to achieve that using Galaxy ? Thanks a lot for your help ! Best,

galaxy • 767 views
ADD COMMENTlink modified 2.3 years ago by Martin Čech ♦♦ 4.9k • written 2.3 years ago by selma.maacha0

Hello, One option would be to use Bowtie2.

You could provide your reference sequence (350 bp, wt version of the locus) in fasta format as the reference genome and allow Bowtie2 to align your reads against that.

BWA could also be used for this application.

Cheers, Mo Heydarian, Galaxy Team

ADD REPLYlink written 2.3 years ago by Mo Heydarian830
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