
CopraRNA - v.2.1.2  - archive README

License: MIT

When using CopraRNA please cite:
Patrick R. Wright, et al. 
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487–E3496

and/or

Patrick R. Wright, et al.
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123

If you run into problems or have any questions, please do not hesitate to
contact us at:
rna@informatik.uni-freiburg.de


-- Archive file explanations

CopraRNA_result.csv:
This is the final result table of your CopraRNA run.
It contains the the amount of predictions specified by the
topcount parameter (def: 200). If less than this amount
of predictions is returned then the the file contains
all possible predictions.

CopraRNA_result_all.csv:
This is the non truncated version of the CopraRNA result.
It contains all possible CopraRNA predictions.

CopraRNA_option_file.txt:
This file contains the set of input options.

16s_sequences.fa/.aln (in Phylogeny):
This is the FASTA file containing the (aligned) 16s sequences that
the phylogeny is calculated on.

compatible.treefile/.fneighbor (in Phylogeny):
These files stores the 16s phylogeny.

compatible.distmat (in Phylogeny):
This file contains the distance matrix for the 16s phylogeny.

zscore.weight/weights.warning:
The unrooted weights for the individual organisms are stored in this file.
If an organism has a weight greater than 0.5 then this is reported in
weights.warning.

cluster.tab:
This tab delimited file contains the clusters of homologous 
protein coding genes throughout the organisms participating 
in the prediction. The clusters are computed with DomClust.

*regions *pdf *ps *png (in Regions_plots):
These image files contain the regions plots of your run.

*.fa.intarna.csv (in IntaRNA):
These files contain the results of the single IntaRNA whole
genome predictions for each organism participating in the analysis.
One of these files is created per organism.

ncrna.fa (in FASTA):
This FASTA contains the sequences you submitted.

*_upfromstartpos_*_down_*.fa (in FASTA):
These FASTA files contain the putative target sequences of the
respective organisms in the prediction.

*tags.clustered*:
These files contain the IntaRNA predictions for for the clusters
of homologous putative targets. _rcsize is the truncated input
for the CopraRNA 1 thread (only if -cop1 was set).

target_sequences_orgofint.fa: (only if -websrv was set // in FASTA)
This FASTA contains the putative target sequences extracted from the
organism of interest's genome. It is a copy of one of the
*_upfromstartpos_*_down_*.fa files. 

coprarna_websrv_table.csv: (only if -websrv was set)
This csv table contains the data for the Freiburg RNA tools webserver frontend.

CopraRNA_result.map_evo_align: (only if -websrv was set)
The file is used to post process the predictions for the webserver frontend.

termClusterReport.txt: (only if -enrich was specified // in Enrichment)
This file contains the DAVID functional enrichment for the amount of
candidates specified in the -enrich parameter.

aux_table.csv: (in Enrichment)
This is the auxilliary enrichment file for the organism of interest.

copra_heatmap.html/copraRNA.json: (in Enrichment)
This html file contains the heatmap for the enriched terms from your prediction.
It can be viewed in your web browser. The json file is needed for correct
display of copra_heatmap.html.

enriched_heatmap_big.*: (in Enrichment)
pdf and png files for the functional enrichment heatmap.

sRNA_conservation_heatmap.pdf:
This file shows the interaction conservation of the top 25 predictions.

evo_alignments.zip:
This archive contains the alignments of the clusters of putative target
sequences with an annotation to visualize the interaction sites and consensus
interaction regions in Jalview.

all_predictions (not made if -cop1):
This directory contains the results for all modes available in CopraRNA 2. 

Rdata:
Precomputed R data environments. 

README.txt:
This file.

