Lastz.... using the xmask option

Question

[mafireyi]

I am trying to compare two genomes by aligning them together using lastz. I have used the following command

lastz path/to/my/assembled/genome/genome.fa[multiple] path/to/other/species/genome/ref.genome.fa.gz > output.maf

this is the error I am getting is;

FAILURE: bad fasta character in /path/to/other/species/genome/ref.genome.fa.gz (ascii 1F)

I am thinking this might me a non-ACGT character error and therefore have to use xmask or nmask.

My question is how do u used xmask?

thanks

[natasha.sernova]

Hello!

As far as I have understood you need to align two genomes from UCSC.

Below you can find their detailed guide for the alignment.

http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto

The mistake you show, "bad fasta character" in many cases means some substitution instead of ">" sign. Check it.

In the web-site above they write about masking the following:

MASKING: Both genomes have to be repeatmasked and masked Tandem Repeat Finder (trf) first

Some people also had problems with LastZ before, like here: Error message using LASTZ in Geneious

I would suggest another tool in case you will not find a source of your problem:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4783527/

Good luck!

Answer 1

[ifreecell]

The bad fasta character error come from non-ACGT characters in your fa files, to avoid this error, you just pass "--ambiguous=iupac" option to lastz, for details see lastz documentation.

lastz genome1.fa genome2.fa --ambiguous=iupac --format=maf > output.maf