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Find all significant local alignments between reads
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genome with 30%GC content #66

Closed hermeseduardo closed 6 years ago

hermeseduardo commented 7 years ago

Hi there,

I am assembling a genome with 30%GC content, using Falcon, 40X coverage. You mentioned that some option made ('If the -b option is set'), alert daligner of a compositional bias, so I just add this option in my pa and ovlp fc_run.cfg, right?

Eg: pa_HPCdaligner_option = -vb -B70 -t16 -e.70 -l1000 -s1000 ovlp_HPCdaligner_option = -vb -B70 -t32 -h60 -e.96 -l500 -s1000

thegenemyers commented 7 years ago

I took it out (the -b option) as it didn't seem to help. At 70% AT it should still be OK albeit long stretches of A and T only can create some bad alignments, but only in a handful of place in our experience with Mediterranus Schmidtae which has a similar compositional bias.

-- Gene

On 9/30/17, 11:47 PM, hermeseduardo wrote:

Hi there,

I am assembling a genome with 30%GC content, using Falcon, 40X coverage. You mentioned that some option made ('If the -b option is set'), alert daligner of a compositional bias, but I can not see it anymore in the most recent version DALIGNER, Is there still something in DALIGNER to 'help' with compositional bias?

Daligner in my fc_run.cfg. pa_HPCdaligner_option = -v -B70 -t16 -e.70 -l1000 -s1000 ovlp_HPCdaligner_option = -v -B70 -t32 -h60 -e.96 -l500 -s1000

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hermeseduardo commented 7 years ago

thanks. Looks like I am working with an old version then since the -b option it is still there. I think that it is interesting since bias composition could be a big deal in the assembly, specially if the PacBio coverage is low, in my case 40X. I will have a go with -b just to see what happens but then will update to the latest version. Because of the low coverage I am also playing with other daligner options, eg. -e. , if you can think of any suggestion it will be appreciated, specially when the long reads gets split because of low coverage. I will asses the assembly later with two libraries of Illumina (80X)