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mostly for issues pertaining to the content of the legumeinfo datastore; may also relate to characteristics of its user interface or managing the mirroring process to the legfed instance
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CDCFrontier.gnm3.ann1.expr.mixed.Sutton_2018a/b have crappy sample identifiers #121

Closed sammyjava closed 2 years ago

sammyjava commented 2 years ago

Presumably these can and should be improved before we load them into ChickpeaMine.

Sutton_2018a

#identifier
L00GEN1_C6AGAANXX_CAGATC_L001
L00GEN1_C6AGAANXX_CAGATC_L002
L00GEN1_C6AGAANXX_CAGATC_L003
etc.

Sutton_2018b

#identifier
P3_C_1_CBBYRANXX_CGCTCATT-ATAGAGGC_L003
P3_C_1_CBBYRANXX_CGCTCATT-ATAGAGGC_L004
P3_C_1_CBBYRANXX_CGCTCATT-ATAGAGGC_L005
P3_C_1_CBBYRANXX_CGCTCATT-ATAGAGGC_L006

The other three sets look pretty good although there some capitalization inconsistency which I'll clean up.

sammyjava commented 2 years ago

I'll track these down with the experimentalists or actually probably just make them up from the tissue+treatment+rep.

sammyjava commented 2 years ago

Created user-friendly IDs as follows:

#identifier     name    description     treatment       tissue  development_stage       species genotype        replicate_group
L00GEN1_C6AGAANXX_CAGATC_L001   GENECTRL1L1     salt control lane 1     non-saline control      leaf            Cicer arietinum Genesis836      Genesis836_salt_control
L00RUP1_C6AGAANXX_ATCACG_L001   RUPACTRL1L1     salt control lane 1     non-saline control      leaf            Cicer arietinum Rupali  Rupali_salt_control

#identifier     name    description     treatment       tissue  development     species genotype        replicate_group
P3_C_1_CBBYRANXX_CGCTCATT-ATAGAGGC_L003 RUPACTRL1L3     Phytophthora control lane 3     control root            Cicer arietinum Rupali  Rupali_Phytophthora_control
P2_C_1_CBBYRANXX_AGCGATAG-TATAGCCT_L003 YORKCTRL1L3     Phytophthora control lane 3     control root            Cicer arietinum Yorker  Yorker_Phytophthora_control

Emailed various authors to get README.description.

sammyjava commented 2 years ago

I'll close this since I fixed the identifiers and harassing the authors isn't part of this issue. Although it is an issue.