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waldronlab / curatedMetagenomicDataCuration

Sample Metadata Curation for curatedMetagenomicData
https://waldronlab.io/curatedMetagenomicDataCuration/
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duplicate samples in NielsenHB_2014 & LeChatelierE_2013 #62

Open luzhang321 opened 2 years ago

luzhang321 commented 2 years ago

Hi :)

The duplicate samples are also mentioned in previous issues. https://github.com/waldronlab/curatedMetagenomicDataCuration/issues/14 https://github.com/waldronlab/curatedMetagenomicDataCuration/issues/8

But I couldn't find the duplicate tables you mentioned in the above issues.

For example, in NielsenHB_2014 and LeChatelierE_2013, MH0001 image

  1. Their information of the reads is the same, but their ERR are different. Does it mean they are the same even with different ERR numbers? It makes me feel really confused here.
  2. In NielsenHB_2014, it is indicated in ena file PRJEB1220 as a mix of hiseq2000 and GA, why here is all hiseq2000? Also LeChatelierE_2013, their ena file indicates the sequencing platform is IlluminaGA and hiseq2000, why in samplemetadata is only hiseq?

Thanks for the help.

The version I used: 3.0.1

lwaldron commented 2 years ago

@paolinomanghi would you respond?

paolinomanghi commented 1 year ago

@AndreaZen-1 can you fix this one?