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Commit 42fc6dc9 authored by Anna Buschart's avatar Anna Buschart
Browse files

add links in readme part1

parent db738768
This repository contains code used in the multiomic analyses of faecal microbiota from four families with several cases of T1DM ( __MuSt__ ).
to build a search data base for [proteomics](proteomics-data-base.md) from predicted proteins and their variants:
* rename4proteomics.pl
* trypsinStartEnd.pl
* variant_annotateRepairedTab.pl
* variants_annotateTab4Stats.pl
* variants_locateType.pl
* [rename4proteomics.pl](rename4proteomics.pl)
* [trypsinStartEnd.pl](trypsinStartEnd.pl)
* [variant_annotateRepairedTab.pl](variant_annotateRepairedTab.pl)
* [variants_annotateTab4Stats.pl](variants_annotateTab4Stats.pl)
* [variants_locateType.pl](variants_locateType.pl)
to parse [functional annotations](functional-annotations.md) of gene predictions (some including [coverage](calculating-coverage.md)):
* 150310_MUST_hmmBestAll.py
* 150705_MUST_hmmParse.py
* 150705_MUST_hmmParsePfam.py
* consolidate_hmmscan_results.pl
* consolidate_hmmscan_results_justKEGG.pl
* 150705_MUST_keggParseNW.py
* ko2des_clean.txt
* calculateCoverageAndGaps2.pl
* 150322_bestHmmReadParse.py
* 150415_bestHmmAveCovParse.py
* 150630_keggReadParse.py
* [150310_MUST_hmmBestAll.py](150310_MUST_hmmBestAll.py)
* [150705_MUST_hmmParse.py](150705_MUST_hmmParse.py)
* [150705_MUST_hmmParsePfam.py](150705_MUST_hmmParsePfam.py)
* [consolidate_hmmscan_results.pl](consolidate_hmmscan_results.pl)
* [consolidate_hmmscan_results_justKEGG.pl](consolidate_hmmscan_results_justKEGG.pl)
* [150705_MUST_keggParseNW.py](150705_MUST_keggParseNW.py)
* [ko2des_clean.txt](ko2des_clean.txt)
* [calculateCoverageAndGaps2.pl](calculateCoverageAndGaps2.pl)
* [150322_bestHmmReadParse.py](150322_bestHmmReadParse.py)
* [150415_bestHmmAveCovParse.py](150415_bestHmmAveCovParse.py)
* [150630_keggReadParse.py](150630_keggReadParse.py)
to annotate phylogenetic [marker genes with the taxonomy](annotate-phylogenetic-marker-genes.md) of the best hit from the mOTU database:
* fastaExtractWithCoordBase1.pl
......
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