Closed msimbirsky closed 5 years ago
Could you point me to the project that you run the test? Also, the swiss army knife will correct only the leading and trailing N of the scaffold, but not the enzyme recognition site that still mix up in Bionano NCBI output, right?
That's right. The project is here: https://platform.dnanexus.com/projects/FVkzY180G2V1pxZYPKFJKxyx/monitor/job/FVzGpz80G2V4zPP81bxJpp2G
This looks good, @msimbirsky . I just don't have a chance to validate your sed
command because your input doesn't have such event. Also, I notice that the unscaffold output from Bionano has 'NNNN' in it which surprised me. Maybe they came from scaff10x. I didn't have access to your original input fasta (file-FVj19Xj0b7ZKGQpBBXy2K251), so I can't tell what is going on. If you didn't use 10x scaffold as input, maybe we should ping Arang and the rest to investigate.
@Arkarachai I do not see any N's in the input fasta file so they must be added by Bionano. Possibly from the restriction enzyme sites.
The NNN is present in the first sequence. dx cat project-FVkzY180G2V1pxZYPKFJKxyx:file-FVzKXk80j2zYYjvq4160x20y | zcat | less
Scaff10x_0_subseq_13154162_13245134_obj I see at least two of them in the If the NNN is added by Bionano, I'm a bit surprised whey they call this unscaffold. Could you grant me access to the input files? file-FVj19Xj0b7ZKGQpBBXy2K251 file-FQ03XKQ0b7ZJBxKb4Bgk9qqj
The inputs are in the project bCatUst1
project which is shared with org-vgp
. Are you part of this org? If not you should ask Arang to be added.
I will go ahead and published the new app versions since the unscaffolded issue is unrelated.
Add a command to Bionano apps that removes the colon character added into contig names and refactor the apps to use latest coding best practices