Hello Community,
I recently performed a pairwise genome-wide alignment of two species using Lastz (https://lastz.github.io/lastz/, v1.04.03). Following are the steps that I followed for performing the alignments:
1) split the genomes into chromosomes and store them in different files using csplit:
csplit species1.fa '/^>/' "{*}" --prefix=species_name_ --suffix-format="%d.fa"
2) Use the following Lastz command to go over every possible pairs of chromosomes and generate outputs in .maf format:
lastz $i $j --gap=x --inner=x --gappedthresh=x --ambiguous=iupac --scores=x --transition --output=alignment_chains/
basename $i .fa-basename $j .fa.maf --format=maf+ --chain &
(I put 'x' to indicate numeric values that go in those positions - originally those entries are numbers and not 'x')
The output that I get are .maf files and all the entries (alignment chains) from the reference genome are exclusively from the positive strand, while that is not the case for the query genome (which has both positive and negative strand). My question is as follows:
Is it the case the alignments consists of negative strand of the reference as well, however just for the sakes of consistency (?) these entries are present in the files as their corresponding entries on the positive strand? If so, then how can I tell which entries are from negative strand? Or is it that Lastz exclusively gives me alignments from the positive strand and not the negative, if so then how can I change this?
Any help in this regard will be highly appreciated!
