changing the representative genome

[ngarud]

Hi Stephen,

I want to change the representative genome used for calling SNPs for one of the species. I just wanted to confirm that the only two files that need to be updated using info from PATRIC are:

midas_db_v1.2/rep_genomes/Bacteroides_uniformis_57318/genome.features.gz
midas_db_v1.2/rep_genomes/Bacteroides_uniformis_57318/genome.fna.gz

Does midas_db_v1.2/genome_info.txt need to be updated too?

Thanks,
Nandita

[snayfach]

Hi Nandita, No, I don't think the genome_info.txt needs to be updated. Let me know if you get any errors and I can help. Thanks, Stephen

…

On Fri, May 5, 2017 at 11:15 AM, Nandita Garud ***@***.***> wrote: Hi Stephen, I want to change the representative genome used for calling SNPs for one of the species. I just wanted to confirm that the only two files that need to be updated using info from PATRIC are: midas_db_v1.2/rep_genomes/Bacteroides_uniformis_57318/genome.features.gz midas_db_v1.2/rep_genomes/Bacteroides_uniformis_57318/genome.fna.gz Does midas_db_v1.2/genome_info.txt need to be updated too? Thanks, Nandita — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#54>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACAbrdD7rvy0PhmtqPMUwueVXpYWSrRQks5r22c4gaJpZM4NSQEV> .

[ngarud]

Thanks! On Fri, May 5, 2017 at 11:17 AM, Stephen Nayfach <notifications@github.com> wrote:

…

Hi Nandita, No, I don't think the genome_info.txt needs to be updated. Let me know if you get any errors and I can help. Thanks, Stephen On Fri, May 5, 2017 at 11:15 AM, Nandita Garud ***@***.***> wrote: > Hi Stephen, > > I want to change the representative genome used for calling SNPs for one > of the species. I just wanted to confirm that the only two files that need > to be updated using info from PATRIC are: > > midas_db_v1.2/rep_genomes/Bacteroides_uniformis_57318/genome.features.gz > midas_db_v1.2/rep_genomes/Bacteroides_uniformis_57318/genome.fna.gz > > Does midas_db_v1.2/genome_info.txt need to be updated too? > > Thanks, > Nandita > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#54>, or mute the thread > <https://github.com/notifications/unsubscribe-auth/ ACAbrdD7rvy0PhmtqPMUwueVXpYWSrRQks5r22c4gaJpZM4NSQEV> > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#54 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB_n2JdT7RsO7Y2hfP7mf8vQyXEwMWplks5r22fNgaJpZM4NSQEV> .

[ngarud]

One more question -- suppose I run the SNP calling module in MIDAS with the --species_id flag. Do the number of reads that map to the desired species change in contrast to when MIDAS is run with all species (i.e. --species_id flag is not used)?

Thanks,
Nandita

[snayfach]

Probably a bit depending on how related the species are in the community. I wouldn't worry too much about it.

I did this this a while back. Specifically, I compared consensus trees built by MIDAS using --species_topn 1 to --species_topn 20 for one species. The phylogenetic placements were nearly identical.

[snayfach]

I'm closing this, but reopen if you run into any error in the code