Hello, I have performed a lot of next gen sequencing, but am very new to the genome browser and the associated file formats. I am trying to understand what exists in this area and have a few basic questions.
I am interested in writing tools to display SNP and other feature data as custom tracks in some genome browser. Some of these features will have insertions relative to the reference. I would like to use custom non-human reference sequences (viral genomes). If possible, in some contexts I'd also like to use an AA sequence as the reference, which is distinct from displaying a NT reference with the translations displayed. Most of my information about supported file formats has come from this page: http://genome.ucsc.edu/FAQ/FAQformat.html Here are the questions: 1. Based on the above page, it seems that Personal Genome SNP format is the best and possible only option to display indels relative to the reference. Is this true? If not, how are short insertions (1-12nt) usually represented? 2. I have been able to find very little in terms of creating custom reference sequences using UCSC genome browser. I am assuming that if i did a local install, this would be possible. Are there resources on this topic I did not find? Can anyone comment on the process of adding custom reference sequences? 3. Are there any capabilities to use an AA sequence as the reference. It appears that a translation track can be shown; however, that's not quite the same as a purely AA alignment. There's already a lot to digest, and the simpler I can make the view the better. 4. I am also considering NCBI's sequence viewer for this project: http://www.ncbi.nlm.nih.gov/projects/sviewer/ The advantages I see with the NCBI viewer are that it will support many references, and can show AA alignments. Does anyone have experience with this and do you have comments comparing it to the UCSC genome browser? Thanks in advance for any help. I tried to research these in advance, and apologize if I missed some obvious resources that answered these. -Ben Bimber _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
