[wgs-assembler-users] fastqToCA and fastaToCA conversion confusion

[Jens H. <jen...@go...>]

Hi,

I have converted a number of 454 reads in FASTQ format and Sanger reads in FASTA format. For the Sanger reads I have generated my own quality value file (as well in FASTA format).

I called the conversion routines as follows:

Sanger Library:
./fastaToCA -l BES_random_shear_library_reverse -s <pathtofasta>/BES_random_shear_library_reverse -q <pathtoqual>/BES_random_shear_library_reverse.qlt > <outpath>/BES_random_shear_library_reverse.frg

454 Library:
./fastqToCA -insertsize 2834 172 -libraryname F7HI6DR01-corrected -technology 454 -mates <pathtofastq>/F7HI6DR01-corrected.fastq > <outpath>/F7HI6DR01-corrected.frg

What strikes me here, is that the conversion of my Sanger library results in an FRG file where the fields seq: and qlt: are filled, while the conversion of my 454 library doesn't. This especially confusion to me because when I dump a FRG file "after" running the assembly using the command

gatekeeper -dumpfrg -allreads assembly.gkpStore > asm.frgs

The frg file is filled with the assumably correct sequences and quality values, even though I only used converted FASTQ files for the assembly. Is this an expected behaviour?

Thanks in advance for any help on that matter.


fastaToCA Conversion Result: please find BES_random_shear_library_reverse.frg