Answers.Body: <p>I asked the same question on the ipdSummary GitHub page and I got the following response:</p>
  <p>&quot;I think that was an experimental option that was never fully working or validated, and it no longer works. We probably need to update the help text. Use the separate tool jasmine if you want to do m5C calling.&quot;</p>
  <p>jasmine also is a tool in the SMRT toolkit that analyzes the kinetic signatures of cytosine bases in CpG motifs to identify the presence of 5mC.</p>
  
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Answers.UserDisplayName: Marjan
Answers.Body: <p>@Marjan We have Pacbio sequence files and we would like to extract methylation information of these files.I would like to ask if you know any software or are familiar with what steps should be done afterwards.</p>
  
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Answers.Text: This would not constitute as an answer, please create a new post with your question. Also, doing some literature reading could give you ideas on how to deal with the data.
Answers.UserDisplayName: Karthik Nair
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Answers.Text: You can detect methylation information using ipdSummary with the argument --identify. 
  The command in my question is detecting methylation too.
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Answers.UserDisplayName: María José
Body: <p>I have installed the latest SMRT Tools (ipdSummary version 3.0). My goal is to extract ipdRatio and modified bases. In the ipdSummary --help command :</p>
  <pre><code>--identify IDENTIFY   Specific modifications to identify (comma-separated list). Current options are m6A, m4C, m5C_TET. Using --control overrides this option. (default: m6A,m4C)
  </code></pre>
  <p>Accordingly, I am running this command:</p>
  <pre><code>ipdSummary sorted_chr21_000.bam --reference $REF_path/$REF_FILE_NAME.fasta --referenceWindow 20:1-200000 --identify m6A,m4C,m5C_TET -j 20 --methylFraction --outfile $save_path/$chrom/$name
  </code></pre>
  <p>My bam file is sorted and relatively small (&lt;200 MB).
  But this command never finishes and does not throw any errors. In different stages of working it just stops. I checked different thread numbers and smaller files, but still, the command doesn't work.
  However, once I changed 'm5C_TET' to 'm5C' it worked perfectly fine and very fast on the same bam file, but in the output, I could not see any information on 'm5C' modifications. I checked the new command with many other bam files and still the same.</p>
  <p>My question is the following:
  How can I get at least 'm5C' modifications? Should I change my SMRT Tools version?</p>
  
Tags: <pacbio>
Title: ipdSummary command stops working if --identify m5C_TET is included in command, and does not give any m5C info either
ThreadText: # ipdSummary command stops working if --identify m5C_TET is included in command, and does not give any m5C info either
  
  (Asked by: username_0 on 2024-01-24)
  
  I have installed the latest SMRT Tools (ipdSummary version 3.0). My goal is to extract ipdRatio and modified bases. In the ipdSummary --help command :
  
  ```
  --identify IDENTIFY   Specific modifications to identify (comma-separated list). Current options are m6A, m4C, m5C_TET. Using --control overrides this option. (default: m6A,m4C)
  
  ```
  
  Accordingly, I am running this command:
  
  ```
  ipdSummary sorted_chr21_000.bam --reference $REF_path/$REF_FILE_NAME.fasta --referenceWindow 20:1-200000 --identify m6A,m4C,m5C_TET -j 20 --methylFraction --outfile $save_path/$chrom/$name
  
  ```
  
  My bam file is sorted and relatively small (<200 MB).
  But this command never finishes and does not throw any errors. In different stages of working it just stops. I checked different thread numbers and smaller files, but still, the command doesn't work.
  However, once I changed 'm5C\_TET' to 'm5C' it worked perfectly fine and very fast on the same bam file, but in the output, I could not see any information on 'm5C' modifications. I checked the new command with many other bam files and still the same.
  
  My question is the following:
  How can I get at least 'm5C' modifications? Should I change my SMRT Tools version?
  
  **Tags:** pacbio
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2024-01-25. Score: 0 | Accepted answer
  
  I asked the same question on the ipdSummary GitHub page and I got the following response:
  
  "I think that was an experimental option that was never fully working or validated, and it no longer works. We probably need to update the help text. Use the separate tool jasmine if you want to do m5C calling."
  
  jasmine also is a tool in the SMRT toolkit that analyzes the kinetic signatures of cytosine bases in CpG motifs to identify the presence of 5mC.
  
  
  ---
  
  ### Answer by username_1 on 2024-08-29. Score: 1
  
  @username_0 We have Pacbio sequence files and we would like to extract methylation information of these files.I would like to ask if you know any software or are familiar with what steps should be done afterwards.
  
  > **Comments:**
  > **username_2**: This would not constitute as an answer, please create a new post with your question. Also, doing some literature reading could give you ideas on how to deal with the data.  
  > **username_0**: You can detect methylation information using ipdSummary with the argument --identify.  The command in my question is detecting methylation too.  
  
  ---
  
  