Hello,
total beginner in genomics and bioinformatics.
We have modified HEK293 in our lab and we sequenced its Whole Genome (Pacbio long reads, mapped on hg38).
I would like to identify the parental cell line and compare the mutations of our cells compared to the references HEK293 cells.
The website http://hek293genome.org provides the information of the references cell lines (mapped on hg18). I can't download the whole genome but we have access to the SNP files readable with IGV.
What would be the smartest strategy to be able to make the comparison ?
In summary we have:
- Whole genome of our cells mapped on hg38 (.bam file)
- SNP and mutations of our cells (.vcf file)
- SNP of reference cells (.vcf file)
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Thank you for your attention!
Use the galaxy platform MiModD tools to do SNP mapping. Here is a protocol that roughly follows Doitsidou, 2010 which I used on C. elegans:
Remove adapter sequences on the raw reads with the Cutadapt tool set to use Paired-end reads (depends what sort of sequencing you did) before alignment against a reference genome sequence using the Map with BWA-MEM tool.
Put the output BAM format file was put through the MiModD Reheader tool to change the sample name before performing variant calling using the MiModD Variant Calling tool with the reference genome set to the one rom the previous step.
The resulting bcf format file is used as the input for the MiModD Extract Variant Sites tool using an independently generated vcf data set.
Linkage maps are then generated using the MiModD NacreousMap tool to visualize the genomic region of interest before using MiModD Rebase Sites to realign the vcf file to any more modern annotation of the genome (http://hgdownload.soe.ucsc.edu/goldenPath/ is a good source) as the input chain file.
The realigned vcf file then has the variants annotated using the SnpEff eff tool with a reference genome from the SnpEff download tool as the genome source before MiModD VCF Filter is applied to focus on the genomic region of interest which is then visualized with the MiModD Report Variants tool.
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