Answers.Body: <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>
  
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Answers.CreationDate: 2019-09-12T14:19:25.650Z
Answers.Text: This would be a very good alternative. Thanks a lot @terdon for the answer.
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Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-12T14:15:02.047Z
Answers.LastActivityDate: 2019-09-12T14:15:02.047Z
Answers.UserDisplayName: terdon
Body: <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>
  
Tags: <phylogenetics><bowtie2><crispr>
Title: Read alignment using Bowtie2
ThreadText: # 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 @username_1 for the answer.  
  
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