Tophat Colorspace Fastq Format

Question

[Jetse]

Does anyone know in which format Tophat wants his fastq format for colorspace data?

I tried sanger format, fake colorspace and combined csfasta and qual files, but all give errors. When using csfasta files with separate quality files tophat works fine.

Answer 1

[Ashutosh Pandey]

I have never used Tophat for color space alignment but when I use SHRiMP it also asks me to input the colorspace sequence in fastq format. I use Brent's code to trim and convert the csfasta files to fastq format. Here is the link: https://github.com/brentp/bio-playground/blob/master/solidstuff/solid-trimmer.py . BTW, there is also a script that basically does the same thing (conversion) and it comes with the BFAST package.

[Jetse]

I tried this program, to retrieve the reads for bowtie (the program tophat uses), this returns me separate csfasta and quality files. So I think this means Tophat cannot handle fastq colorspace, so I can not use our own java XSQ converter...

[Ashutosh Pandey]

I am not sure what you are trying to say. i dont think any program will take combined csfasta and quality file. these shud be two separate files. Also, xsq converter can give you both colorspace fastq format or csfasta and quality files. though I have never used it for the colorspace fastq format but it atleast gives you an option.