tophat - solexa options

[sohnic]

Hi,
Does anyone known where to find information about the following tophat options:
--solexa-quals
--solexa1.3-quals

I have to align fastq reads (100 nt) issued from a “Hi-Seq 2000” on a reference genome. The data analysis pipeline is HiSeq Control Soft. v. 1.1.37.8 RTA 1.7.48 CASAVA 1.7. So, I'm not sure that the option solexa-quals is the good one in my case ("TopHat was designed to work with reads produced by the Illumina Genome Analyzer").

Thank you,

S.

[maubp]

Are you familiar with the three (sequence space) FASTQ variants? See:
http://dx.doi.org/10.1093/nar/gkp1137

The type of quality scores from Solexa/Illumunia changed in v1.3 from Solexa to PHRED (different log mappings), and their FASTQ encoding will change again in CASAVA v1.8 to the original Sanger style.

http://seqanswers.com/forums/showthread.php?t=8895

[sohnic]

Hi,
Thanks a lot for those very interesting informations.
So, I thing I have to use the solexa1.3-quals option in my case.
To be sure, I've asked the sequencing society. I'm waiting their answer...

Thanks again for your help,

S.

[ttnguyen]

It might be helpful to check the encoding by looking at your FASTQ files. fastQC can do that very quick.

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

[sohnic]

Hi,
The sequencing compagny confirms the use of the solexa1.3-quals option.
And, fastQC, that seems to be a really good application says the same thing (solexa>1.3).
Many thanks !

S.