Origin of unmapped reads

Question

[Kay]

Hi,

i have reads that did not map to my reference genome. I used -f 4 to extract the unmapped reads and blastn them back to my reference genome again, and it appears all the reads still align to my reference genome. I dont understand why thy did not map initially.

Any ideas are welcome!

[lieven.sterck]

Can you some more details to your question? What commands/software did you use, what is your input data, what is your threshold for the blast analysis, ... things like that. Without that info it's hard to provide a meaningful answer.

it is very well possible that a read gives a blastn hit but does not get aligned given the read-mapper parameter settings though

[dthorbur]

I agree with the other comment, checking a few random reads with BLAST is a good starting point. But the unmapped reads could simply reflect an accumulation of differences between the reference genome population and the one you sampled. Do you have an idea of the evolutionary difference between the reference and sample?