ELAND and circular genomes?

[ewilbanks]

Hi all,

OK, so I'm pretty sure this is a silly question, but I haven't been able to find a definitive answer!

When using ELAND to map reads against a circular genome, how does it deal with those reads at the very end? In other words, if your genome is 3,000,000 bp long, what happens to a 30 bp read that aligns to the region 2,999,998 - 28 ?

Thanks!
Lizzy

[francesco.vezzi]

Actually I don't know the exact answer but I think that ELAN takes in input a reference sequence and it consider it as string with an end and a beginning. So if there is a read spanning between the end and the beginning I think it will not find it, the only possibility is the existence of an option for circular genomes.

If There is no this option you can put at the end of your circular genome a piece long as a read taken from the beginning. In this way you will find the reads in which you are interested. Doing this thing you have only to pay attention at the repeated reads that you can generate.

[ewilbanks]

I seem to have found the answer to this for paired end options in eland_extended:

--circular

This causes pickBestPair to treat each chromosome as circular and not
linear, enabling it to detect valid pairings that “wrap around” when the two
alignments are mapped onto the linear representation of the chromosome.

still hunting about what it does with regular reads!