Can I analyze *.csfasta & *.xsq data on Galaxy ?
Hi, I am working on the colorspace data. I have one old data (*.csfasta, SOLiD4) & one new (*.xsq, 5500xl). I wanted to use tophat and cufflinks pipelines with Galaxy, Although tophat can make use of colorspace data, but galaxy seems to be accepting only FASTQ format for most of its tools. And the online community is strongly discouraging the conversion of colorspace to FASTQ. So, is there any work-around for this problem ? Do I have to modify the scripts according to my requirement in my local installation ? Looking forward for your advise. Thanks in advance, Nikhil. -- ------------------------------------------------------------ Nikhil Vinod Mallela, M.Sc. University of Muenster, Institute of Bioinformatics, Neil-Stensen Str. 12-14, 48149, Muenster,Germany. Tel.: +49 0251 83 50006 Fax: +49 0251 83 53005Email: mallela@uni-muenster.dehttp://complex-systems.uni-muenster.de/-------------------------------------...
On Wednesday, August 7, 2013, Nikhil Mallela wrote:
Hi,
I am working on the colorspace data. I have one old data (*.csfasta, SOLiD4) & one new (*.xsq, 5500xl). I wanted to use tophat and cufflinks pipelines with Galaxy, Although tophat can make use of colorspace data, but galaxy seems to be accepting only FASTQ format for most of its tools. And the online community is strongly discouraging the conversion of colorspace to FASTQ.
What is bad is converting FASTA without qualities to FASTQ with made up qualities, regardless of if this is sequence or color space.
So, is there any work-around for this problem ? Do I have to modify the scripts according to my requirement in my local installation ?
Do you have the quality scores for your data, in a *.qual file normally. Peter
Hi Peter,
What is bad is converting FASTA without qualities to FASTQ with made up qualities, regardless of if this is sequence or color space. I am a newbie to this. I didn't know about this. I was under the impression that 'conversion is bad whether one has the qual files or not!' Thanks for the input.
Do you have the quality scores for your data, in a *.qual file normally. Yes, I do have the *.qual files with me. I've tried to convert my data into FASTQ on my local installation but I was unsuccessful.
I've used this tool under NGS:QC and manipulation, and used my *.qual & *.csfasta files as an input. [image: Inline image 1] The tool didn't give me any error, but there was nothing inside the data set that is generated. PFA for further info from the [image: Inline image 4] button. [image: Inline image 3] So, could you pls suggest me something on what to do about this ? Thanks, Nikhil.
participants (2)
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Nikhil Mallela -
Peter Cock