Answers.Body: <p>I downloaded genome from <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1/</a> I got 5 files in it so if you are confused which one to use in that so GCF.fna having genomic data with fna extension is used as an reference genome if you are also new to this things this might be useful.</p>
  <p>Thank you</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-07T14:29:11.677Z
Answers.Text: Please accept the other answer as well, as it addressed your question and was given before you added your own answer and accepted just the one you added
Answers.UserDisplayName: Ram RS
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Answers.CreationDate: 2023-08-07T05:41:05.270Z
Answers.LastActivityDate: 2023-08-07T05:41:05.270Z
Answers.UserDisplayName: Moon
Answers.Body: <p>What you need is the genome sequence in fasta format, typically suffixed <code>.fa</code>, for example from <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1/</a></p>
  <p>This file needs to be indexed via <code>bwa index</code>.</p>
  
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Answers.CreationDate: 2023-08-02T20:03:15.353Z
Answers.LastActivityDate: 2023-08-02T20:03:15.353Z
Answers.UserDisplayName: ATpoint
Body: <p>I want to do mapping with bwa mem. I downloaded a reference genome from ncbi database which is (Danaus plexippus). I got one <code>ncbi_database.zip</code> file which contain 2 folders and 3 files of doc,assembly_report_json file. I read one file named <code>read.md</code> which came after downloading but its not helping. What should be done in this case?</p>
  <p>I don't have an issue with using bwa-mem; the problem is with the reference genome from NCBI. I downloaded it from <a href="https://ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1" rel="nofollow noreferrer">https://ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1</a> but after that I checked the downloaded file and I got 5 folders into it and I'm confused which one to use. 2 files have <code>.fna</code> extension and the rest are reports that are in the json file format.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-02T13:22:44.053Z
Comments.Text: Welcome to the site @moon. My role is to try to get the questions as clear as possible. Firstly it's worth noting **bwa-mem2**, but you want to try getting `bwa mem` working first. The **read.md** will just be the installation instructions. Are you looking for the manual? Is the following helpful, https://hcc.unl.edu/docs/applications/app_specific/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands/ and follow the `bwa mem` instructions. Maybe try it and then post back on specifically what the problem is, e.g. the error message?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-02T21:48:27.193Z
Comments.Text: The answer by @atpoint is the best answer to the question as the question is written right now. My advice is to consider accepting this and further questions can then be asked. This Lepidoptera genome assembly and a reference genome is definitely needed.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-04T00:16:49.157Z
Comments.Text: Only accept answers if they solve the problem you're having. If the answers don't match your problem, feel free to clarify the question to explain further.
Comments.UserDisplayName: gringer
Tags: <read-mapping><reference-genome><bwa><ncbi>
Title: Reference genome (bwa -mem)
ThreadText: # Reference genome (bwa -mem)
  
  (Asked by: username_0 on 2023-08-02)
  
  I want to do mapping with bwa mem. I downloaded a reference genome from ncbi database which is (Danaus plexippus). I got one `ncbi_database.zip` file which contain 2 folders and 3 files of doc,assembly\_report\_json file. I read one file named `read.md` which came after downloading but its not helping. What should be done in this case?
  
  I don't have an issue with using bwa-mem; the problem is with the reference genome from NCBI. I downloaded it from <https://ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1> but after that I checked the downloaded file and I got 5 folders into it and I'm confused which one to use. 2 files have `.fna` extension and the rest are reports that are in the json file format.
  
  **Tags:** read-mapping, reference-genome, bwa, ncbi
  
  > **Comments:**
  > **username_1**: Welcome to the site @username_0. My role is to try to get the questions as clear as possible. Firstly it's worth noting **bwa-mem2**, but you want to try getting `bwa mem` working first. The **read.md** will just be the installation instructions. Are you looking for the manual? Is the following helpful, https://hcc.unl.edu/docs/applications/app_specific/bioinformatics_tools/alignment_tools/bwa/running_bwa_commands/ and follow the `bwa mem` instructions. Maybe try it and then post back on specifically what the problem is, e.g. the error message?  
  > **username_1**: The answer by @username_4 is the best answer to the question as the question is written right now. My advice is to consider accepting this and further questions can then be asked. This Lepidoptera genome assembly and a reference genome is definitely needed.  
  > **username_2**: Only accept answers if they solve the problem you're having. If the answers don't match your problem, feel free to clarify the question to explain further.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2023-08-07. Score: 0 | Accepted answer
  
  I downloaded genome from <https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1/> I got 5 files in it so if you are confused which one to use in that so GCF.fna having genomic data with fna extension is used as an reference genome if you are also new to this things this might be useful.
  
  Thank you
  
  > **Comments:**
  > **username_3**: Please accept the other answer as well, as it addressed your question and was given before you added your own answer and accepted just the one you added  
  
  ---
  
  ### Answer by username_4 on 2023-08-02. Score: 1
  
  What you need is the genome sequence in fasta format, typically suffixed `.fa`, for example from <https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009731565.1/>
  
  This file needs to be indexed via `bwa index`.
  
  
  ---
  
  