Question: Tophat Colorspace Fastq Format
0
gravatar for Jetse
6.6 years ago by
Jetse0
Jetse0 wrote:

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.

tophat format fastq • 2.3k views
ADD COMMENTlink modified 6.6 years ago by Ashutosh Pandey11k • written 6.6 years ago by Jetse0
0
gravatar for Ashutosh Pandey
6.6 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

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.

ADD COMMENTlink written 6.6 years ago by Ashutosh Pandey11k

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...

ADD REPLYlink written 6.6 years ago by Jetse0

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.

ADD REPLYlink written 6.6 years ago by Ashutosh Pandey11k
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