Closed ilevade closed 5 years ago
Hi,
I'm running Desman on multiple gut microbiome samples and I'm trying to identify different species which are not E. coli.
I am stuck at this step of the pipeline, when you want to identify the core COGS:
"Then we determine those regions of the contigs with core COGs on in single copy using the 982 predetermined E. coli core COGs:
$DESMAN/scripts/SelectContigsPos.pl $DESMAN/complete_example/EColi_core_ident95.txt < ClusterEC.cogs > ClusterEC_core.cogs"
How do you generate the "EColi_core_ident95.txt" file ? I probably missed a step, but I couldn't find the information in the protocol.
In other DESMAN tutoriels, I saw this file was called scgs.txt. But it wasn't described how to generate it.
Thank you so much for your help !
Hi,
I'm running Desman on multiple gut microbiome samples and I'm trying to identify different species which are not E. coli.
I am stuck at this step of the pipeline, when you want to identify the core COGS:
"Then we determine those regions of the contigs with core COGs on in single copy using the 982 predetermined E. coli core COGs:
$DESMAN/scripts/SelectContigsPos.pl $DESMAN/complete_example/EColi_core_ident95.txt < ClusterEC.cogs > ClusterEC_core.cogs"
How do you generate the "EColi_core_ident95.txt" file ? I probably missed a step, but I couldn't find the information in the protocol.
In other DESMAN tutoriels, I saw this file was called scgs.txt. But it wasn't described how to generate it.
Thank you so much for your help !