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aldob / iMUT-seq

Analytical scripts for the iMUT-seq manuscript that is currently in preparation
MIT License
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Custom genome in bowtie2 alignment #1

Open Chemical118 opened 10 months ago

Chemical118 commented 10 months ago

Thanks for the good material. I have a question about the alignment using bowtie2, here according to mutation_sequencing_analysis_script.sh when you did the bowtie2 alignment you used hg38 as a custom genome obtained using bedtools getfasta. But I don't understand how to do this, could you help me with this?

aldob commented 9 months ago

Thanks for the good material. I have a question about the alignment using bowtie2, here according to mutation_sequencing_analysis_script.sh when you did the bowtie2 alignment you used hg38 as a custom genome obtained using bedtools getfasta. But I don't understand how to do this, could you help me with this?

Hello, sorry for the very late reply. Reference genomes are in the form of fasta files. To create a custom genome that only contained the genomic regions I was amplifying in the experiment, I used bedtools getfasta to retrieve the regions of the genome I was amplifying in fasta format. This fasta was then used as the reference genome in my bowtie2 alignments.

It is possible to align iMUT-seq reads to the whole genome, however this takes significantly longer than aligning to a custom genome and also has increased misalignment rates.