General Frequently Asked Questions
There are on the Project page.
Use the following web page : Venny demo page
When you download an available gz file, the web server re-zip it (it's independent to our development) but the file you have is name file.gz. If you want to access to the data rename it file.gz.gz and unzip it twice.
RNAseqDeNovo Frequently Asked Questions
Have a look on our project documentation page.
Use the martform and select "sequence" attribute as output.
Since March 2013, a contigs are prefixed by species name (max 3 letters), then the name of the best annotation gene, then 2 numbers the second is the number of contigs named with this gene the first the current index of this gene. e.g. DR_SACB.3.10 correspond to the third contig on ten with the gene name SACB.
We perform an exact fisher test for each gene, adjust the p-value with FDR correction (Benjamini and Hochberg, 1995) and identifie in which pool it's up or down regulated by comparing the frequence.
Those kind of analysis are not implemented. Download the count file named merged_count.csv in download tabs and use R.
The JBrowse View may don't work, please send an email to celine.noirot@toulouse.inra.fr with an example of the error. An alternative solution is to download bam files and annotation file in gff format, and use IGV on your desktop.
% Qcoverage or Q-cov : Percentage of the query length covered by the alignemnt (all hsps between the contigs and the subject)
% Scoverage or S-cov : Percentage of the subject covered by the alignemnt (all hsps between the contigs and the subject)
% Qidentities or ident: Percent of identity for the complete alignment (all hsp between the contigs and the subject)
% Identity : Percent of identity for the HSP alignment
% Qcoverage : Percent of conserved aa for the complete alignment (all hsp between the contigs and the subject)