Answers.Body: <p>The breakdown would be:</p>
  
  <ul>
  <li>1.5-2 GB per sample for fastq files.</li>
  <li>~3GB per BAM file, depending on the aligner</li>
  </ul>
  
  <p>So ~5GB per BAM file, which is about 50GB total. That can vary by maybe 20%, depending on how compressible the results are (I rearrange our fastq files to make them more compressible, so I'm probably underestimating what others would see).</p>
  
  <p>Obviously using Salmon/Kallisto would halve the storage requirements. Using CRAM would also decrease things, though obviously fewer tools support it.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-23T11:12:23.290Z
Answers.Text: So, for a whole genome sequencing that would roughly 15 TB?
Answers.UserDisplayName: Zizogolu
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-23T11:21:34.730Z
Answers.Text: You would need  600-750 million pairs for a human genome (mostly depending on the fragment size), which is 20-25 times as much data.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-23T14:50:11.610Z
Answers.Text: Maybe it is for a different question but how do you rearrange the fastq to make them more compressible? Is there some paper or blog to read on this?
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-23T15:04:57.740Z
Answers.Text: @llrs It's a by-product of using `clumpify` (from BBTools) to remove optical duplicates. The process involves sorting fastq files such that similar reads are near each other, which means the resulting files compress more than they would otherwise. I run that as part of our normal Illumina demultiplexing pipeline.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-24T08:18:53.270Z
Answers.Text: Ok, then it might be out of my scope (I usually get the demultiplexed files). Thanks for the tip!
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-23T11:09:28.357Z
Answers.LastActivityDate: 2019-01-23T11:09:28.357Z
Answers.UserDisplayName: Devon Ryan
Body: <p>Supposing upcoming RNA-seq for 3 conditions and 3 replications for each, how much is data storage requirements?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-23T10:54:14.750Z
Comments.Text: What sort of sequencing depth and read length?
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-23T11:02:01.313Z
Comments.Text: Thank you let's say 75pb, paired end and 30X
Comments.UserDisplayName: Zizogolu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-23T11:03:26.053Z
Comments.Text: I assume you mean 30 million reads (pairs really), since 30X is meaningless for RNA-seq.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-23T11:11:40.380Z
Comments.Text: Sorry I am very bad in these staffs :( thank you for correcting me
Comments.UserDisplayName: Zizogolu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-23T13:55:31.047Z
Comments.Text: Please add all the extra information to your question since comments are easy to miss and can be deleted without warning. Also please clarify what species you will be working on since that can radically affect how much space you will need.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-23T13:57:36.873Z
Comments.Text: Thank you, I am not sure about how many samples and what experiments we are going to run yet. As soon as I obtained more information I will elaborate my post
Comments.UserDisplayName: Zizogolu
Tags: <r><rna-seq>
Title: data storage requirements for RNA-seq and WGS
ThreadText: # data storage requirements for RNA-seq and WGS
  
  (Asked by: username_0 on 2019-01-23)
  
  Supposing upcoming RNA-seq for 3 conditions and 3 replications for each, how much is data storage requirements?
  
  **Tags:** r, rna-seq
  
  > **Comments:**
  > **username_1**: What sort of sequencing depth and read length?  
  > **username_0**: Thank you let's say 75pb, paired end and 30X  
  > **username_1**: I assume you mean 30 million reads (pairs really), since 30X is meaningless for RNA-seq.  
  > **username_0**: Sorry I am very bad in these staffs :( thank you for correcting me  
  > **username_2**: Please add all the extra information to your question since comments are easy to miss and can be deleted without warning. Also please clarify what species you will be working on since that can radically affect how much space you will need.  
  > **username_0**: Thank you, I am not sure about how many samples and what experiments we are going to run yet. As soon as I obtained more information I will elaborate my post  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-01-23. Score: 3
  
  The breakdown would be:
  
  * 1.5-2 GB per sample for fastq files.
  * ~3GB per BAM file, depending on the aligner
  
  So ~5GB per BAM file, which is about 50GB total. That can vary by maybe 20%, depending on how compressible the results are (I rearrange our fastq files to make them more compressible, so I'm probably underestimating what others would see).
  
  Obviously using Salmon/Kallisto would halve the storage requirements. Using CRAM would also decrease things, though obviously fewer tools support it.
  
  > **Comments:**
  > **username_0**: So, for a whole genome sequencing that would roughly 15 TB?  
  > **username_1**: You would need  600-750 million pairs for a human genome (mostly depending on the fragment size), which is 20-25 times as much data.  
  > **username_3**: Maybe it is for a different question but how do you rearrange the fastq to make them more compressible? Is there some paper or blog to read on this?  
  > **username_1**: @username_3 It's a by-product of using `clumpify` (from BBTools) to remove optical duplicates. The process involves sorting fastq files such that similar reads are near each other, which means the resulting files compress more than they would otherwise. I run that as part of our normal Illumina demultiplexing pipeline.  
  > **username_3**: Ok, then it might be out of my scope (I usually get the demultiplexed files). Thanks for the tip!  
  
  ---
  
  