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LAST FAQ
========
:Q: Why does LAST sometimes miss strong alignments?
:A: This is because it avoids getting huge numbers of repetitive
alignments, by just finding a few strongest matches for each part
of each query sequence. To find more repetitive matches, increase
the ``lastal -m`` parameter, e.g. ``-m100``.
..
:Q: Why does LAST sometimes show two separate alignments, and
sometimes one merged alignment, between the same sequences?
:A: This is because LAST forbids highly dissimilar regions inside
alignments, but the maximum-allowed dissimilarity depends on the
alignment score / E-value threshold (which depends on the database
size). For more details, please see the discussion of "X-drop" in
`Parameters for accurate genome alignment`_.
..
:Q: Does it matter which sequence is used as the "reference" (given to
lastdb) and which is used as the "query" (given to lastal)?
:A: It may do. In short, LAST tries hard to find alignments for every
position in the query. When mapping reads to a genome, you
probably want the genome to be the reference, and the reads to be
the query. That way, for each read, it will search for several
most-similar locations in the genome. The other way, for each
location in the genome, it will search for several most-similar
reads. As another example, if you compare a genome to a library
of repeat sequences, you probably want the genome to be the query
and the repeat library to be the reference.
..
:Q: How can I get the percent-identity of each alignment?
:A: Use lastal option -fBlastTab, or use maf-convert.
..
:Q: Why is LAST so slow at reading/writing files?
:A: Probably because the files are huge and your disk is slow (or lots
of people are using it). Try to use a reasonably fast disk.
Typically, after reading a large file once, subsequent reads of
the same file are much faster, because the operating system caches
it.
lastal reads files into shared memory using "mmap", and this
occasionally seems to have trouble, notably on "advanced" file
systems (Lustre and GlusterFS).
On one Linux system, the above-mentioned cache occasionally got
into some kind of bad state, making lastal very slow. This was
solved by running the following command (as root)::
echo 1 > /proc/sys/vm/drop_caches
..
:Q: How does LAST get the sequence names? How can I get nice, short,
unique names?
:A: The first whitespace-delimited word in the sequence header line is
used as the name. You can arbitrarily customise the names using
standard Unix tools. For example, this will replace each FASTA
name with a unique serial number::
awk '/>/ {$0 = ">" ++n}; 1' queries.fasta | lastal myDb
This will do the same for FASTQ (assuming 4 lines per record,
i.e. no line wrapping)::
awk 'NR % 4 == 1 {$0 = "@" ++n}; 1' queries.fastq | lastal myDb
Sometimes you can make LAST's output significantly smaller by
shortening the names.
..
:Q: How can I find alignments with > 95% identity?
:A: One way is to use a scoring scheme like this: +5 for a match, and
-95 for a mismatch or a gap::
lastal -r5 -q95 -a0 -b95
RAQ (Rarely Asked Questions)
----------------------------
:Q: Why does lastal hang forever on my quad processor system?
:A: This problem was reported once, and was fixed by prefacing the
command with::
numactl --interleave=all
.. _Parameters for accurate genome alignment: https://doi.org/10.1186/1471-2105-11-80
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