a general issue---testing with real data

[GoogleCodeExporter]

Hi all,

as you know I started to  test the aligners both with simulated and real data. 
It comes that the simulation tool is able to generate directly FASTQ files (and 
not solexa.txt). So we have two different kind of data: the original generated 
from the sequencer (.txt) and the FASTQ.

As you know the vast majority of the modules have been developed starting from 
.txt, some of them starting from them starting from the fastq, and the reason 
is that some tools have internal routines that do the conversion, others have 
not.

BTW, with the sim data I started with BOWTIE SE. As the simulated data are 
fastq I have customized my pipeline removing the conversion step and adjusting 
the parameters accordingly. The validation is ok, but the process doesn't work 
and I have got errors with no streams.

I am also attaching the pipe I modified...am I doing something wrong? It is 
important for me as I have to modify many pipes to test those fastq.


Tks,

Fed

Original issue reported on code.google.com by [email protected] on 20 Sep 2011 at 6:22

Attachments:

• [Screen shot 2011-09-20 at 11.19.22 AM.png](https://storage.googleapis.com/google-code-attachments/informatics/issue-25/comment-0/Screen shot 2011-09-20 at 11.19.22 AM.png)
• BOWTIE_SE_30millions_sim_from_fastq.pipe

[GoogleCodeExporter]

I looked at your workflow and there doesn't seem to be anything wrong with it. 
It runs fine for me on fgene1. Since you are running these on fgene3 and are 
getting errors, I suspect it is a server related error but I don't have access 
to fgene3 to verify this.

Original comment by [email protected] on 22 Sep 2011 at 8:06

[GoogleCodeExporter]

Yes , you are right..I am quite happy because it means that the pipe was 
ok...:) I'm running it on fgene2

Fed

Original comment by [email protected] on 22 Sep 2011 at 8:12