alignment software and ref sequence
We are currently using MAQ to align our Solexa reads to our reference sequence. Does anyone know if MAQ can also tell me which parts of my reference sequence have no reads aligned to them? If not, can anyone suggest a program that can tell me this info? Thanks!
-
-
Pretty sure MAQ can't, and a quick scan of the man page didn't yield anything.
Have you tried one of the visualization tools? Only one I know off the top of my head is tablet, but unfortunately haven't had a chance to play with it myself:
--
Senthil Palanisami -
Actually, if I am not wrong, Maq`s pileup output has a column with the number of reads aligning at a given position, so you can get those with a 0 coverage out
HTH,
DaveLast edited by dnusol; 01-18-2010, 03:23 AM.Comment
-
MIRA does. Can even give back a list of genes and/or intergenic regions which are hit by this (if references sequence has annotations like, e.g., a GenBank). If you're working with 20 to 30m reads, have a look at it.Originally posted by mlee View Post
Beware, being a de-novo assembler, it's a lot more memory intensive than other mapping programs when used for mapping only.
Regards,
B.
Disclaimer: I wrote MIRA. It's useful to me but it might not be for you. Feedback appreciated.
Comment
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment