[galaxy-user] tophat issues

2013-11-30 Thread miroslav.sotak 

To whom it may concern

I do have a problem with tophat. I can easily put fastq data to 
history and according to RNA-seq Analysis Exercise provided by Jeremy. 
We checked the type of Ascii ofset for the quality estimation. I tried 
even quality data converter set to 33 (we do have data of this ASCII 
offset from 2 different sources) but tophat for Illumina simply can 
not read the data before and even after quality format converter. We do 
not have any idea what is going on. I am logged in Galaxy with current 
email, can you check my data and is there any converter for quality 
offset?


Sincerely
Miro Sotak
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[galaxy-user] Transcriptome Hypericum perforatum

2013-11-25 Thread miroslav.sotak 


To whom it may concern

I would like to kindly ask you if you do have any experience in de-novo 
transcriptomic analysis (no reference genome available) who might give 
us some advice.
Our main question is how to create the best set of cDNA contigs, on 
which we can map our RNAseq reads for the analysis of differential 
expression. Currently 4 larger sets of of RNAseq reads are available 
from different genotypes as well as draft genome assembly for one of the 
genotypes. We worry about the SNPs in different genotypes affecting the 
assembly, if we combine all the RNAseq datasets and using assemblers 
such as Trinity, Oases, Velvet. Might it be better to use the draft 
genomic assembly to obtain cDNA contigs using Tophat/cufflinks via all 
available RNAseq data or only using the RNAseq data from the same 
genotype as the genome draft?


Thank you in advance
Best wishes
Miro Sotak
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