Re: [galaxy-user] Large local file of NGS for FASTAQ Groomer

Arthur, When the data is coming from casavA 1.8 (actually I believe from 1.5 and above) I think it's already in the proper format. An excellent overview is here: http://en.wikipedia.org/wiki/FASTQ_format Basically the headers of the fastq reads are my indication at the moment. Since 1.8 it change

[galaxy-user] Make a vcf file

Hi, This may be a dense question, but how do we generate a vcf file from the public version of Galaxy? Am I missing something obvious? Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine

[galaxy-user] filtering pile-up fails

Dear All, I have been successful by using the online tool to align Illumina pair end reads , each direction 5GB, and also generated a pileup of 680,000,000 lines, but the filtering of the pileup always fails, it runs for several hours and I get an empty file back. I tried different options and dif

Re: [galaxy-user] Solution for: Error running cuffdiff. Error: cannot open reference GTF file CONDITION, CONTROL for reading

> The problem ended being the use of "Perform Bias Correction"(-b) and a > GTF file with no "Database/Build" associated. Looking at cuffdiff > wrapper I found, if a FASTA reference is not selected from the > history, the FASTA reference of the GTF file associated build is used. > If there is not bu

[galaxy-user] Clustering with cuffcompare or cuffdiff results

Dear Sir or Madam, I am planning to do clustering of several libraries based on the output of cuffcompare or cuffdiff, as they allow me to construct a matrix whose columns represent the libraries and rows are the count of transcripts or genes. I want to construct the matrix because it is the r

Re: [galaxy-user] Clustering with cuffcompare or cuffdiff results

> 1. It seems that it is better to run everything up to cuffdiff, but does > cuffdiff allow multiple sample comparison because I read somewhere that even > for multi-samples it still compare tham pairwisely? Cuffdiff supports replicate analysis. > In a sense, because I want to do clustering whi

Re: [galaxy-user] filtering pile-up fails

Hello Sebahattin, It may be that the data is too large to run on the Galaxy public instance, which means that a local or cloud instance would be the next recommendation, as explained in this wiki: http://wiki.g2.bx.psu.edu/Big%20Picture/Choices But, before you make the investment of moving yo

Re: [galaxy-user] bug for mate pairs colorspace to sequence conversion

Hi Philipp, Sorry for the delay in reply, the question is a bit confusing since the conversion tools allow for the adapter base to be specified (and the default is a G). I am not sure we are talking about the same tool, so to clear things up, would you please send a shared history link and any