absolute k-mer coverage explained (Abyss)

[harrb]

The (very limited) Abyss manual explains the fasta headers in the contigs assembly outfile like this:


>n iii jjjj
Where n is the numeric contig ID, iii is the contig length in nucleotides, and jjjj is the absolute k-mer coverage.

I don't understand what "absolute k-mer coverage" means. Can someone maybe explain? But what I would really like to know is which basepair in a contig are represented by how many reads. IS there a way to get this from the k-mer coverage?

THANKS

[boetsie]

Hi harrb,

have a look at this older thread about the header;

http://seqanswers.com/forums/showthread.php?t=7005&highlight=abyss+coverage

About the coverage (per position on the contig i think you mean?) you can probably run ABYSS with the option

--coverage-hist=FILE

This option (as stated at http://seqanswers.com/wiki/ABySS) records the k-mer coverage histogram in FILE. Though, I'm not 100% sure, since i can not test it @tm .

Otherwise, you can map your reads to the contigs (Bowtie, BWA), producing a .sam file. Convert the .sam file to .bam file and do;

samtools pileup -f your_ref.fa your.bam

Have a look at this thread;

http://seqanswers.com/forums/archive/index.php/t-7679.html

Good luck,
Boetsie