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Forum: Bioinformatics 12-19-2010, 01:45 PM
Replies: 1
Views: 5,794
Posted By harrb
absolute k-mer coverage explained (Abyss)

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...
Forum: Bioinformatics 12-10-2010, 07:40 AM
Replies: 0
Views: 1,748
Posted By harrb
another question about pileup format

Hello again,

I have another question concerning the pileup format as produced by samtools afterr calling SNPs. I could not find what an ">" means in the "bases" column (column 9) in the outfile....
Forum: Bioinformatics 12-10-2010, 07:37 AM
Replies: 2
Views: 3,338
Posted By harrb
thanks. I did this but just could not understand...

thanks. I did this but just could not understand how a site can be called heterozygous when it is only represented by one read.
Forum: Bioinformatics 12-09-2010, 11:36 AM
Replies: 2
Views: 3,338
Posted By harrb
SAMTOOLS SNP calling question


I have used tophat to map my paired-end Solexa reads to the mouse genome. I have called the SNPs using samtools and below is an exert from the raw outfile.
I wonder about the fact that for...
Forum: Bioinformatics 11-23-2010, 08:45 AM
Replies: 1
Views: 3,172
Posted By harrb
documentation for ABySS


I am a new user of ABySS. I have 50 Million Solexa 100bp paired-end transcriptome reads that I am intending to assemble de novo. Velvet could not handle my dataset, but my first run with...
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