Answers.Body: <p>The codes are usually available at <a href="https://github.com/ENCODE-DCC" rel="nofollow noreferrer">DCC's GitHub</a>.</p>
  <p>You can always email them if you have more questions.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-09-04T11:07:14.913Z
Answers.LastActivityDate: 2020-09-04T11:07:14.913Z
Answers.UserDisplayName: Code42
Body: <p>I am trying to find details for how the ENCODE ChIP seq samples were processed. </p>
  
  <p>Linking to a ChIPseq samples on www.encodeproject.org (e.g. <a href="https://www.encodeproject.org/experiments/ENCSR051DXE/" rel="nofollow noreferrer">https://www.encodeproject.org/experiments/ENCSR051DXE/</a>) offers a PDF "overview" of the pipeline which says basically nothing. The page will also offer you a map of the pipeline, which basically just has headings:
  <a href="https://i.sstatic.net/vVFyS.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/vVFyS.png" alt="enter image description here"></a></p>
  
  <p>Clicking on a step gives you a popup with a link to the "<a href="https://www.encodeproject.org/pipelines/ENCPL220NBH/" rel="nofollow noreferrer">Chip-seq read mapping</a>" pipeline. This just contains the same overview PDF and a link to "<a href="https://www.encodeproject.org/chip-seq/transcription_factor/" rel="nofollow noreferrer">ChIP-seq Data Standards and Processing Pipeline</a>". This page contains again, a vague outline of the pipeline, a link back to the page we just came from and a list of quality control thresholds.</p>
  
  <p>I can't seem to find anywhere the proper details. For example, if BWA was used, was it MEM or aln? What parameters were used for the mapping? One of the steps is read filtering: what where the filters? How were they applied? There is a link to a <a href="https://github.com/ENCODE-DCC/chip-seq-pipeline/blob/master/dnanexus/chip_workflow.py" rel="nofollow noreferrer">github page</a> for running the pipeline on DNAnexus, but I can't make head nor tail of it. </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-24T11:00:39.720Z
Comments.Text: I don't really understand it but perhaps the [tests.sh](https://github.com/ENCODE-DCC/chip-seq-pipeline/blob/master/dnanexus/tests.sh) it might be easier to understand for you (how they call it, what they expect and so on).
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-24T12:02:33.293Z
Comments.Text: They are using `bwa aln` option with `-q 5 -l 32 -k 2`.
  Ref: https://github.com/ENCODE-DCC/chip-seq-pipeline/blob/541dd361f28ef7568f3743c00dfcb882c461df2c/dnanexus/input_shield/dxapp.json line 43
Comments.UserDisplayName: arup
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-24T12:17:13.423Z
Comments.Text: Updated ENCODE ChIP-seq analysis pipeline https://github.com/ENCODE-DCC/chip-seq-pipeline2 . This also features the usage of `bwa aln` Ref: https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/e4d53da91f7dcf16dad984b1c9ebbbf168f8ef4b/src/encode_bwa.py line: 73.
Comments.UserDisplayName: arup
Tags: <encode><reproducibility>
Title: Details of ENCODE processing pipelines
ThreadText: # Details of ENCODE processing pipelines
  
  (Asked by: username_0 on 2018-10-24)
  
  I am trying to find details for how the ENCODE ChIP seq samples were processed.
  
  Linking to a ChIPseq samples on www.encodeproject.org (e.g. <https://www.encodeproject.org/experiments/ENCSR051DXE/>) offers a PDF "overview" of the pipeline which says basically nothing. The page will also offer you a map of the pipeline, which basically just has headings:
  [![enter image description here](https://i.sstatic.net/vVFyS.png)](https://i.sstatic.net/vVFyS.png)
  
  Clicking on a step gives you a popup with a link to the "[Chip-seq read mapping](https://www.encodeproject.org/pipelines/ENCPL220NBH/)" pipeline. This just contains the same overview PDF and a link to "[ChIP-seq Data Standards and Processing Pipeline](https://www.encodeproject.org/chip-seq/transcription_factor/)". This page contains again, a vague outline of the pipeline, a link back to the page we just came from and a list of quality control thresholds.
  
  I can't seem to find anywhere the proper details. For example, if BWA was used, was it MEM or aln? What parameters were used for the mapping? One of the steps is read filtering: what where the filters? How were they applied? There is a link to a [github page](https://github.com/ENCODE-DCC/chip-seq-pipeline/blob/master/dnanexus/chip_workflow.py) for running the pipeline on DNAnexus, but I can't make head nor tail of it.
  
  **Tags:** encode, reproducibility
  
  > **Comments:**
  > **username_1**: I don't really understand it but perhaps the [tests.sh](https://github.com/ENCODE-DCC/chip-seq-pipeline/blob/master/dnanexus/tests.sh) it might be easier to understand for you (how they call it, what they expect and so on).  
  > **username_2**: They are using `bwa aln` option with `-q 5 -l 32 -k 2`. Ref: https://github.com/ENCODE-DCC/chip-seq-pipeline/blob/541dd361f28ef7568f3743c00dfcb882c461df2c/dnanexus/input_shield/dxapp.json line 43  
  > **username_2**: Updated ENCODE ChIP-seq analysis pipeline https://github.com/ENCODE-DCC/chip-seq-pipeline2 . This also features the usage of `bwa aln` Ref: https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/e4d53da91f7dcf16dad984b1c9ebbbf168f8ef4b/src/encode_bwa.py line: 73.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2020-09-04. Score: 0
  
  The codes are usually available at [DCC's GitHub](https://github.com/ENCODE-DCC).
  
  You can always email them if you have more questions.
  
  
  ---
  
  