search

PacificBiosciences / FALCON

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
Other
205 stars 103 forks source link

Linking input and output (corrected) reads names #258

Open chklopp opened 8 years ago

chklopp commented 8 years ago

Hi,

Could Falcon produce a file linking input and output (corrected) read names?

Cheers,

Christophe

pb-jchin commented 8 years ago

No yet. The data is stored in the daligner's database. It needs some simple scripts to get the information. We will add some tool when we release the fully diploid haplotig separation code FALCON-Unzip.

pb-cdunn commented 8 years ago

Jason, This actually got worse last Friday, when I fixed something for Ben Lerch. In pbsmrtpipe, when we combine .bam reads into a single .fasta, fasta2DB quits because the "movie" names are not consistent. Until I have time to separate movies into different fasta files, I have added the -p MOVIENAME flag to fasta2DB. So we cannot even match dazzlerdb data back to the reads anymore.

Internal link:

pb-jchin commented 8 years ago

Understood. It just more tedious for downstream code to take the responsibility if we don't get it easier from the upstream.

Sent from my iPhone

On Jan 11, 2016, at 8:17 AM, Christopher Dunn notifications@github.com<mailto:notifications@github.com> wrote:

Jason, This actually got worse last Friday, when I fixed something for Ben Lerch. In pbsmrtpipe, when we combine .bam reads into a single .fasta, fasta2DB quits because the "movie" names are not consistent. Until I have time to separate movies into different fasta files, I have added the -p MOVIENAME flag to fasta2DB. So we cannot even match dazzlerdb data back to the reads anymore.

Internal link:

— Reply to this email directly or view it on GitHubhttps://github.com/PacificBiosciences/FALCON/issues/258#issuecomment-170601172.