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So this is related to CRISPR-CAS9. I am working with off-target predictions for my thesis and was looking at all scientific papers related to CRISPR. I found one and decided to use their datasets. The datasets were not available directly and the method used to obtain them was specified which I had mentioned below:

They have around 30 sgRNAs which are each 23bp long and are aligning the sgRNAs to human reference genome with a tolerance of upto 6 mismatches using Bowtie2.

In order to access the exact dataset, I thought I need to replicate the method they used. To do so, I collected the sgRNAs from their paper and tried to use Bowtie2 to align them against human genome with upto 6 mismatches.

Since my laptop does not have the capacity to perform this operation (it has 8GB RAM), I am searching for interfaces that provide access to Bowtie2. I found Galaxy to be useful. Does anyone know of any other tool that provides an option for Bowtie2?

Thanks!

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One possible workaround would be to blast your sequences against the genome. Then, when you have found where they align, you can extract those regions only into a new fasta file (make sure to take a few kb around each target region) and then use that fasta file as the "genome" you pass to bowtie2.

That would give bowtie a far smaller file to work with and should reduce the memory needed significantly.

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  • $\begingroup$ This would be a very good alternative. Thanks a lot @terdon for the answer. $\endgroup$ – Ina Sep 12 '19 at 14:19

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