Is it possible to create a consensus sequence from a fasta file?

[ssnowfox]

Hello,

The fasta file includes DNA sequences of a target region generated from a pooled sample, is there any way to create a consensus sequence for this region using the fasta file?

Thanks a lot!

[GenoMax]

You could also do the "Reads_Of_Insert" protocol on SMRTportal to get consensus sequences for each insert for a PacBio run. If that is what your question was referring to.

Otherwise, you can do simple multiple sequence alignment using an appropriate program using fasta files and generate a consensus that way.

[lingling huang]

no combined/ subdirectory

Hello, any help will be appreciated! After running tofu_wrap.py, the result directory clusterOut have no combined/ subdirectory. I am confused.Due to my sever is high-powered single-node computer, i can't install SGE and i have no sge setting in my command.Is there some problem? Thank you so much.
My command is below:
tofu_wrap.py --nfl_fa isoseq_nfl.fasta --ccs_fofn reads_of_insert.fofn --bas_fofn input.fofn -d clusterOut --quiver --gmap_db /zs32/data-analysis /liucy_group /llhuang/Reflib/gmapdb --gmap_name hg19 isoseq_flnc.fasta final.consensus.fa

[bowhan]

the "combined" means to combine output from different size bins (it is recommended to sequence cDNAs in different sizes separately to avoid loading bias).
In ToFU, you can and probably should use the option `--bin_manual` to manually separate the inputs into different bins, such as `--bin_manual "(0,2,4,6,8,10,22)"`. I suspect that once you add this option back you should see the "combined" output— it has nothing to do with `--use_sge`. But of course, you should always check the log files to make sure your job finishes successfully.

[lingling huang]

Unfortunately, It doesn't work. In tofu Tutorial #2 Isoform level clustering, example command for using tofu_wrap.py doesn't include option "--bin_manual",but the output result have conbined/ subdirectory. https://github.com/PacificBioscience...-and-Quiver%29
Moreover,"--bin_manual" can determine the size bins in kb,and can create several bins you selected,but seems not combined output from each size bin.