<p>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.</p>

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

CC BY-SA 4.0
2019-09-12T14:19:25.650Z
This would be a very good alternative. Thanks a lot @terdon for the answer.
Ina
CC BY-SA 4.0
2019-09-12T14:15:02.047Z
2019-09-12T14:15:02.047Z
terdon
<p>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:</p>
<p>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.</p>
<p>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.</p>
<p>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 <a href="https://usegalaxy.eu/" rel="nofollow noreferrer">Galaxy</a> to be useful. Does anyone know of any other tool that provides an option for Bowtie2?</p>
<p>Thanks!</p>

<phylogenetics><bowtie2><crispr>
Read alignment using Bowtie2
# Read alignment using Bowtie2

(Asked by: username_0 on 2019-09-11)

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](https://usegalaxy.eu/) to be useful. Does anyone know of any other tool that provides an option for Bowtie2?

Thanks!

**Tags:** phylogenetics, bowtie2, crispr

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## 1 answers

### Answer by username_1 on 2019-09-12. Score: 0

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.

> **Comments:**
> **username_0**: This would be a very good alternative. Thanks a lot @terdon for the answer.  

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