how to obtain a scf or abi or similar file starting with a fastq file and the frequencies of the bases

Question

[msapaydin]

I have a bam file as well as a sample file that displays the frequency with which every base is read at each location. How do I convert these into a chromatogram file format so that I can view this using common chromatogram viewing tools? I have found converters from bam to fastq and some bioperl code that suggests conversion from fastq to scf however the latter step (Converting A Dna Sequence To Abi Or Scf Format) did not work. Thanks.

[Devon Ryan]

Do you want to see pseudo chromatograms for each read or do you just want to look for over/under abundance of bases by position across all of the reads? In the latter case, it'd be easier to just graph that not bother with chromatogram software. In the former case, you're unlikely to actually want to do that.

[msapaydin]

I would like to visualize using Sanger chromatograms the following kind of data:

position A    C    T    G
1        0    5    0    0
2        0    0    50   0
3        0    25   25   0
4        10   0    0    0

[Devon Ryan]

So across all samples then. Just graph that, since shoe-horning that into a chromatogram would be more effort than it's worth.

[msapaydin]

Is there a tool/software to do this? Also how to associate this with an exon model (do we need a chromatogram then?)

edit: found this. http://dsp.stackexchange.com/questions/2828/plotting-dna-chromatogram-trace-data

[Devon Ryan]

The simplest solution would be to just use FastQC, which produces a graph of base composition per position across reads. You could also do that with a bit of scripting in any language.

Chromatograms don't make any sense for looking at quality across reads in NGS. Just look at the phred score distribution.