Colorspace alignment visualization

[zee]

Hi Community,

I am not entirely satisfied with what's available for whole-genome browsing of color space alignments.

I have tried IGV and had a look at the SOLiD alignment browser but I have run into some problems

I have a sorted BAM file from BFAST and I'm not sure how to change this to the Bioscope GFF3 format.

Has anybody had better luck in properly displaying colorspace alignments to a reference genome? I would like to see SNPs, sequencing errors, etc. in colorspace as compared to the reference sequence.

[lvaruzza]

You can open the sorted BAM file in IGV (http://www.broadinstitute.org/igv/)

[zee]

I've been using IGV all this time. It works fine although what I mean is that I would like to be able to view the actual base-pair detail at the highest resolution.
Perhaps it is the structure of my BAM file but I guess I will need to consult the IGV support team if it is an issue.

[NextGenSeq]

Probably not want you are looking for since it's commercial but CLCBio's Genomic Workbench shows the basepair detail, original color space call and quality values in the alignment contigs.

[zee]

Thanks NextGenSeq. That is exactly what I'm looking for but I guess not in a commercial package

Probably not want you are looking for since it's commercial but CLCBio's Genomic Workbench shows the basepair detail, original color space call and quality values in the alignment contigs.

[martian_bob]

Are you willing to do a bit of programming? You can view the BAM file in SAM format (see the manual), send the output to a file, run a program to decode the colorspace bits, and then go from there...