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create_compil's Introduction

create_compil

Pipeline for creating compil database for gut microbiome metaproteomics

create_compil's People

Contributors

stuppie avatar janicexu avatar

Watchers

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create_compil's Issues

Add new data sources

Done:

Food
https://docs.google.com/spreadsheets/d/11TXjYjJelW26wPHQw6Fzl7rtHc-LzCuDihbzfktuC78/edit?usp=sharing

peptide standard peptide sequences
https://www.lifetechnologies.com/order/catalog/product/88320

P00000 Pierce Peptide Retention Time Calibration Mixture
SSAAPPPPPRGISNEGQNASIKHVLTSIGEKDIPVPKPKIGDYAGIKTASEFDSAIAQDKSAAGAFGPELSRELGQSGVDTYLQTKGLILVGGYGTR
GILFVGSGVSGGEEGARSFANQPLEVVYSKLTILEELRNGFILDGFPRELASGLSFPVGFKLSSEAPALFQFDLK

A Catalogue of the Mouse Gut Metagenome
http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP
http://www.nature.com/nbt/journal/v33/n10/full/nbt.3353.html
Xiao, L., et al., A catalog of the mouse gut metagenome. Nat Biotech, 2015.
33(10): p. 1103-1108.

To do

Copied from bitbucket issues [https://bitbucket.org/sulab/metaproteomics/issues/1/changes-to-next-compil-version link]

  • Add integer ID to SeqDB records (so each peptide will have a unique int ID)
  • For every forward protein entry in protdb, add field linking to reverse's protdb ID
  • store sequence hashes and taxid in ProtDB
  • make use of gpff files

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