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snayfach / MIDAS

An integrated pipeline for estimating strain-level genomic variation from metagenomic data
http://dx.doi.org/10.1101/gr.201863.115
GNU General Public License v3.0
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changing the representative genome #54

Closed ngarud closed 7 years ago

ngarud commented 7 years ago

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 commented 7 years ago

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 notifications@github.com 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 https://github.com/snayfach/MIDAS/issues/54, or mute the thread https://github.com/notifications/unsubscribe-auth/ACAbrdD7rvy0PhmtqPMUwueVXpYWSrRQks5r22c4gaJpZM4NSQEV .

ngarud commented 7 years ago

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 notifications@github.com 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 https://github.com/snayfach/MIDAS/issues/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 https://github.com/snayfach/MIDAS/issues/54#issuecomment-299538186, or mute the thread https://github.com/notifications/unsubscribe-auth/AB_n2JdT7RsO7Y2hfP7mf8vQyXEwMWplks5r22fNgaJpZM4NSQEV .

ngarud commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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