Getting a larger consensus sequence from alignments

[Peter O'Reilly]

Hello,

I am new to bioinformatics and am trying to export my consensus sequence (roughly 5 MB) from IGV. When I attempt to "copy consensus sequence" for the entire genome it give an error that states no more than 1 MB can be copied. 

However, even when zooming in to reduce the number of nucleotides copied, it does not seem to work, I simply get nothing copied to the clipboard (no error message). I suspect this is due to the program not being able to load in the consensus sequence on that many nucleotides (the current maximum seems to be 44 KB).

 Is there a way for me to increase the number of nucleotides I can copy at a time? Can the code of the program be altered manually to allow a larger swath of the genome to be visible at a time? If not, is there a recommended program that I can use? Any help is appreciated! 

Best,

Peter O'Reilly 

[igv-help]

You can increase the visibility window for alignments, see the user guide.   However your computer might not be able to handle 1 MB of alignments, but its worth a try.   In general IGV is a visual tool and not well suited for this kind of bulk analysis.   I'm not familiar with what else might be available, but I suspect there is a better tool for this.

[Peter O'Reilly]

Thank you for the response! I will look at the user guide more thoroughly. We have a new lab computer with fairly powerful specs, it may be able to pull it off. 

Peter