Answers.Body: <p>Probably not. ENA doesn't have any ability to specifically flag a file as 2D, and the nanopore file formats have changed a lot, so you pretty much need to rely on the submitter to separate out the reads in a meaningful way.</p>
  
  <p>Also, there wasn't really any consistent convention for what ONT used in their read headers. Looking at some of my old files they had a plain sequence ID (i.e. without anything suggesting temp/comp) in different template/complement folders in the FAST5 files for the components of a 2D read and the consensus sequence, but later changed it to _2D_template and _2D_complement as in the example you have (possibly with an intermediate _1D_template and _1D_complement format). Parsing/understanding those FAST5 files can be difficult, which is why poretools was created in the first place.</p>
  
  <p>It's still a bit of a mess, with the 1D$^2$ reads ending up in a Frankenstein-like state that's partially 1D and partially 2D.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-02-15T22:29:59.420Z
Answers.LastActivityDate: 2018-02-15T22:29:59.420Z
Answers.UserDisplayName: gringer
Body: <p>I am looking at some <a href="https://www.ebi.ac.uk/ena/data/view/SAMEA2757769" rel="nofollow noreferrer">yeast ONT data</a> from <a href="https://www.nature.com/articles/s41598-017-03996-z" rel="nofollow noreferrer">De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms, Giordano et al 2017</a>. </p>
  
  <p>I noticed that the Minion fastq files have both a forward and reverse file. The methods paper says that these reads are from the SQK-MAP006 and SQK-MAP007 protocols which both appear to be 2D. Are these just the 2D forward and reverse files?</p>
  
  <p>Still being unsure, I checked if this was true by counting the number of characters in each read. </p>
  
  <pre><code>&gt;&gt; zcat ERR1883385_1.fastq.gz | head -1
  @ERR1883385.1 dc5b9de2-ba00-47ab-b698-8ad470704c0a_Basecall_2D_000_template EVO107591_Sanger_FAA52213_CBS432_Phenol_3a_4517_1_ch251_file44_strand/1
  
  &gt;&gt; zcat ERR1883385_2.fastq.gz | head -1
  @ERR1883385.1 dc5b9de2-ba00-47ab-b698-8ad470704c0a_Basecall_2D_000_template EVO107591_Sanger_FAA52213_CBS432_Phenol_3a_4517_1_ch251_file44_strand/2
  
  
  &gt;&gt; zcat ERR1883385_1.fastq.gz | head -2 | awk '{ print length($0); }' -
  147
  1675
  
  &gt;&gt; zcat ERR1883385_2.fastq.gz | head -2 | awk '{ print length($0); }' -
  147
  1693
  </code></pre>
  
  <p>As you can see, the read is the same but the forward and reverse strands are different lengths. </p>
  
  <p>Is there some way to just download the <code>poretools</code> equivalent to  <code>2D</code> from ENA without having to download the fast5 files and extract them myself?</p>
  
Tags: <minion>
Title: ENA minion 2D data doesn't actually have 2D data
ThreadText: # ENA minion 2D data doesn't actually have 2D data
  
  (Asked by: username_0 on 2018-02-15)
  
  I am looking at some [yeast ONT data](https://www.ebi.ac.uk/ena/data/view/SAMEA2757769) from [De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms, Giordano et al 2017](https://www.nature.com/articles/s41598-017-03996-z).
  
  I noticed that the Minion fastq files have both a forward and reverse file. The methods paper says that these reads are from the SQK-MAP006 and SQK-MAP007 protocols which both appear to be 2D. Are these just the 2D forward and reverse files?
  
  Still being unsure, I checked if this was true by counting the number of characters in each read.
  
  ```
  >> zcat ERR1883385_1.fastq.gz | head -1
  @ERR1883385.1 dc5b9de2-ba00-47ab-b698-8ad470704c0a_Basecall_2D_000_template EVO107591_Sanger_FAA52213_CBS432_Phenol_3a_4517_1_ch251_file44_strand/1
  
  >> zcat ERR1883385_2.fastq.gz | head -1
  @ERR1883385.1 dc5b9de2-ba00-47ab-b698-8ad470704c0a_Basecall_2D_000_template EVO107591_Sanger_FAA52213_CBS432_Phenol_3a_4517_1_ch251_file44_strand/2
  
  >> zcat ERR1883385_1.fastq.gz | head -2 | awk '{ print length($0); }' -
  147
  1675
  
  >> zcat ERR1883385_2.fastq.gz | head -2 | awk '{ print length($0); }' -
  147
  1693
  
  ```
  
  As you can see, the read is the same but the forward and reverse strands are different lengths.
  
  Is there some way to just download the `poretools` equivalent to `2D` from ENA without having to download the fast5 files and extract them myself?
  
  **Tags:** minion
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-02-15. Score: 2 | Accepted answer
  
  Probably not. ENA doesn't have any ability to specifically flag a file as 2D, and the nanopore file formats have changed a lot, so you pretty much need to rely on the submitter to separate out the reads in a meaningful way.
  
  Also, there wasn't really any consistent convention for what ONT used in their read headers. Looking at some of my old files they had a plain sequence ID (i.e. without anything suggesting temp/comp) in different template/complement folders in the FAST5 files for the components of a 2D read and the consensus sequence, but later changed it to \_2D\_template and \_2D\_complement as in the example you have (possibly with an intermediate \_1D\_template and \_1D\_complement format). Parsing/understanding those FAST5 files can be difficult, which is why poretools was created in the first place.
  
  It's still a bit of a mess, with the 1D$^2$ reads ending up in a Frankenstein-like state that's partially 1D and partially 2D.
  
  
  ---
  
  