# last-pair-probs

This program reads candidate alignments of paired DNA reads to a genome, and:

1. estimates the distribution of distances between paired reads,

2. estimates the probability that each alignment represents the genomic source of the read.

"Paired" means that the reads come from either end of a DNA fragment, in tail-to-tail orientation:

    5' ---------->................................. 3'
    3' .................................<---------- 5'

Or head-to-head orientation:

    5' .................................----------> 3'
    3' <----------................................. 5'

The program writes the alignments with "mismap" probabilities, i.e. the probability that the alignment does not represent the genomic source of the read. By default, it discards alignments with mismap probability > 0.01.

## Simple usage

Suppose we have paired DNA reads in a file called "interleaved.fastq" (in fastq-sanger format), where the first two reads are paired, the next two reads are paired, and so on. We can align them to the human genome like this:

    lastdb -uNEAR hg human-genome.fasta
    lastal -Q1 -e120 -i1 hg interleaved.fastq > temp.maf
    last-pair-probs temp.maf > out.maf

Suppose we have paired reads in two files, where the two first reads are paired, the two second reads are paired, and so on. We can interleave them like this:

    fastq-interleave x.fastq y.fastq | lastal -Q1 -e120 -i1 hg > temp.maf

## Reads from potentially-spliced RNA molecules

Use the -r option:

    last-pair-probs -r temp.maf > out.maf

Without -r, it assumes the distances between paired reads follow a normal distribution. With -r, it assumes the distances follow a skewed (log-normal) distribution, which is much more appropriate for spliced RNA.

## Efficient usage

The preceding recipes make a potentially-huge temp file, and last-pair-probs reads it twice: first to estimate the distance distribution, and then to estimate alignment probabilities. It is more efficient to estimate the distance distribution from a small sample of the data:

    lastal -Q1 -e120 -i1 hg sample.fastq | last-pair-probs -e

Suppose this tells us that the mean distance is 250 and the standard deviation is 38.5. We can use that to estimate the alignment probabilities:

    lastal -Q1 -e120 -i1 hg all.fastq | last-pair-probs -f250 -s38.5 > out.maf

## Going faster by parallelization

This will run the pipeline on all your CPU cores:

    fastq-interleave x.fastq y.fastq |
    parallel-fastq "lastal -Q1 -e120 -i1 hg | last-pair-probs -f250 -s38.5" > out.maf

It requires GNU parallel to be installed (http://www.gnu.org/software/parallel/).

## Details

- The "distance" between a pair of reads means the distance between their 5' ends. Positive distance indicates tail-to-tail orientation, and negative distance indicates head-to-head orientation. Negative distances are not considered when -r is used, nor for circular chromosomes.

- The program reads one batch of alignments at a time (by looking for lines starting with "# batch"). It assumes there is exactly one DNA read per batch: if it finds more than one, it will complain. The lastal -i1 option ensures there is one query per batch.

- The alignments may be in either format produced by lastal (maf or tabular). They must include header lines (of the kind produced by lastal) describing the alignment parameters.

- If a read name ends in neither "/1" nor "/2", the program appends "/1" if it is the 1st in a pair or "/2" if it is the 2nd.

- It is also possible to supply the alignments in two files:

      lastal -Q1 -e120 -i1 hg x.fastq > temp1.maf
      lastal -Q1 -e120 -i1 hg y.fastq > temp2.maf
      last-pair-probs temp1.maf temp2.maf > out.maf

## Options

> `-h, --help` | Print a help message and exit.
> `-r, --rna` | Specifies that the fragments are from potentially-spliced RNA.
> `-e, --estdist` | Just estimate the distribution of distances.
> `-m M, --mismap=M` | Don't write alignments with mismap probability > M.
> `-f BP, --fraglen=BP` | The mean distance in bp. (With -r, the mean of ln[distance].) If this is not specified, the program will estimate it from the alignments.
> `-s BP, --sdev=BP` | The standard deviation of distance in bp. (With -r, the standard deviation of ln[distance].) If this is not specified, the program will estimate it from the alignments.
> `-d PROB, --disjoint=PROB` | The prior probability that a pair of reads comes from disjoint locations (e.g., different chromosomes). This may arise from real differences between the genome and the source of the reads, or from errors in obtaining the reads or the genome sequence.
> `-c CHROM, --circular=CHROM` | Specifies that the chromosome named CHROM is circular. You can use this option more than once (e.g., -c chrM -c chrP). As a special case, "." means all chromosomes are circular. If this option is not used, "chrM" is assumed to be circular (but if it is used, only the specified CHROMs are assumed to be circular.)
> `-V, --version` | Show version information and exit.

## Tips

- To go faster, try gapless alignment (add -j1 to the lastal options). Often, this is only minusculely less accurate than gapped alignment.

## Reference

For more information, please see this article:

> An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome. Shrestha AM, Frith MC. Bioinformatics 2013 29(8):965-972.