Contig annotation and quantification

[raw937]

Hello,

If I have assembled contigs and just want to annotation/quantify (eggnog4, SEED etc) is that option still available? Not the bins but the contigs directly.
I couldn't find it if it is.

[SilasK]

genes are predicted on all contigs in with atlas run assembly

Annotation is automated in the genecatalog module

Change the source for the gene catalog in the config file.

########################
# Gene catalog
#######################
genecatalog:
  source: contigs
...

Rhen run.
atlas run genecatalog <options> combine_gene_coverages

The advantage is with the genecatalog you have all genes in all samples and the time-consuming annotation is done only once.

[raw937]

Not working.

#no run command
atlas run genecatalog test_1k.fasta combine_gene_coverages
Usage: atlas [OPTIONS] COMMAND [ARGS]...
Try "atlas -h" for help.

Error: No such command "run".

#tried with assemble command
atlas assemble genecatalog test_1k.fasta combine_gene_coverages
[2019-03-14 13:40 CRITICAL] Config not found: /data/friesen/clean/CQ/results/assemblies/subsampled/genecatalog

added this to the end of the file:
########################

SAMPLES

########################
samples: 'pwd'

########################

Gene catalog

#######################
genecatalog:
source: contigs

atlas assemble genecatalog testatlas_contig combine_gene_coverages
[2019-03-14 13:43 CRITICAL] Config not found: /data/friesen/clean/CQ/results/assemblies/subsampled/1k/genecatalog

Do I also need to point to the reads?

[SilasK]

Seems you are using atlas 2.0.0 or less. Try to update and follow the Readme or docs how to use the new API with atlas run. Kind regards Silas And may be subscribe to follow the releases on github. I continue to add minior bug fixes.

…

On Thu, Mar 14, 2019, 21:46 Richard Allen White III < ***@***.***> wrote: Not working. #no run command atlas run genecatalog test_1k.fasta combine_gene_coverages Usage: atlas [OPTIONS] COMMAND [ARGS]... Try "atlas -h" for help. Error: No such command "run". #tried with assemble command atlas assemble genecatalog test_1k.fasta combine_gene_coverages [2019-03-14 13:40 CRITICAL] Config not found: /data/friesen/clean/CQ/results/assemblies/subsampled/genecatalog added this to the end of the file: ######################## SAMPLES ######################## samples: 'pwd' ######################## Gene catalog ####################### genecatalog: source: contigs atlas assemble genecatalog testatlas_contig combine_gene_coverages [2019-03-14 13:43 CRITICAL] Config not found: /data/friesen/clean/CQ/results/assemblies/subsampled/1k/genecatalog Do I also need to point to the reads? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#186 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHLK2kWBZQ8Ff5wZVEnr2h5w00BURaY4ks5vWrU6gaJpZM4b03xk> .

[SilasK]

@raw937 Did you succeed?
How would you use SEED? is there a command line application?

[raw937]

I didn't succeed yet. I have to wait on my HPC admin. I will let you know?
Hmm. I have always wanted to integrate metacyc and SEED to ATLAS. SEED hasn't been updated in a while or metacyc as well. However, I do have older databases that could be used (~2014). I could share. The FOAM database maybe a more useful way to get KOs.
However, I do like eggnog's mapper which is useful.
Databases are very hard to maintain funding. Only Uniprot has been able to maintain the funding over the long term. KEGG, metacyc, cog, nog, etc all pay models or extinct. Its a real crime that we can't maintain funding to keep up with maintaining tools, databases, with the ever growing masses of sequence data.

[SilasK]

Continue discussion on #599