[wgs-assembler-users] Trouble interpreting POSMAP info

[Ivan S. <iva...@gm...>]

Hi everyone!

I have trouble with interpreting the POSMAP data of an assembly.
In short - when I compare the positions of reads that are given in the
asm.posmap.frgctg file with the positions I obtain after aligning the reads
to the assembly in asm.ctg.fasta, I can see no relation between the two.
For alignment, I used both BLASR and BWA-MEM.

Description of what I am doing in more details:
Following this tutorial (
http://wgs-assembler.sourceforge.net/wiki/index.php/Escherichia_coli_K12_MG1655,_using_uncorrected_PacBio_reads,_with_CA8.1)
I assembled the E. Coli genome from a set of PacBio reads, and the results
were exactly as described.
After that, I parsed the asm.posmap.frgctg file to obtain the list of reads
that were actually used in the assembly.
I extracted their original headers from the asm.gkpStore.fastqUIDmap file,
and filtered the initial set of reads, so the resulting set contains only
those reads listed in the asm.posmap.frgctg file.
After that, I used both BLASR with default parameters, and BWA-MEM with
PacBio parameters to align those reads on the contig file asm.ctg.fasta.
I then compared the positions of obtained alignments to the positions that
are reported in asm.posmap.frgctg, and I see no correspondance.

Can anyone provide any insight into this?
Am I missing something?
Or maybe the POSMAP files weren't updated with the rest of Celera?


Thank you for your help!


Best regards,
Ivan Sovic.