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Run AMRFinder on BioProjects #4

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13 tasks done
hollygene opened this issue Mar 15, 2021 · 1 comment
Open
13 tasks done

Run AMRFinder on BioProjects #4

hollygene opened this issue Mar 15, 2021 · 1 comment
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E_coli_AMR

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@hollygene
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hollygene commented Mar 15, 2021 •
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  • QC on BioProject: PRJNA318591
  • AMRFinder on BioProject PRJNA318591
  • QC on BioProject: PRJNA324565
  • AMRFinder on BioProject: PRJNA324565
  • QC on BioProject:PRJNA324573
  • AMRFinder on BioProject: PRJNA324573
  • QC on BioProject: PRJNA481346
  • AMRFinder on BioProject: PRJNA481346
  • QC on BioProject: PRJNA503851
  • AMRFinder on BioProject: PRJNA503851
  • QC on BioProject: PRJNA318589
  • AMRFinder on BioProject: PRJNA318589
  • Download sequences for each
@hollygene hollygene created this issue from a note in E_coli_AMR (In progress) Mar 15, 2021
@hollygene
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Steps:

  1. Download list of accessions from Bioproject:
    used this resource: https://www.ncbi.nlm.nih.gov/sra/docs/sradownload/
  2. Search bioproject ID on bioproject website, click on the number of links corresponding to "SRA Experiments", then from that new page click "send to" at the top of the page, select "File" and then "Accession List", save this file somewhere (mine usually goes to downloads folder)
  3. Make sure to rename it something useful like "bioprojectID_acc_list.txt"
  4. Then use FileZilla to upload this to the AHDC server
  5. Use script "get_SRR_data.sh" in Github Cornell Postdoc repository
    • replace everywhere PRJ.... is and run on screen (takes a while)

@hollygene hollygene moved this from In progress to Done in E_coli_AMR May 12, 2021
@hollygene hollygene mentioned this issue May 20, 2021
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