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christophertbrown / iRep

scripts for estimating bacteria replication rates based on population genome copy number variation
MIT License
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Gene-based binning #21

Open annekup opened 6 years ago

annekup commented 6 years ago

I have obtained bins with a gene-based binning, these genes are generally short (<5 kb). Is it possible to apply iRep to this kind of data?

When running it on my data I noticed that iRep can not be calculated (n/a), but un-filtered iRep is estimated. Does the un-filtered iRep take all fragments into account (also <5kb)?

Thanks for your help! Anne

christophertbrown commented 6 years ago

Hi Anne,

iRep will not work with that kind of data. The more fragmented a genome becomes, the more error is introduced. Running iRep on genes is like having a very fragmented genome. iRep has a built in check for genome fragmentation and does not report iRep values for genomes with more than 175 fragments per megabase, which is probably why you are getting the 'n/a' result.

Is it possible to get the assembled scaffolds that contain the genes, and use those for your iRep analysis?

Chris

On Jun 5, 2018, at 12:28 AM, annekup notifications@github.com wrote:

I have obtained bins with a gene-based binning, these genes are generally short (<5 kb). Is it possible to apply iRep to this kind of data?

When running it on my data I noticed that iRep can not be calculated (n/a), but un-filtered iRep is estimated. Does the un-filtered iRep take all fragments into account (also <5kb)?

Thanks for your help! Anne

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annekup commented 6 years ago

Hi Chris, thanks for your reply. I want to compare several metagenomes and have individual assemblies for each of them. Thus I could take the scaffolds from the individual assemblies that contain a majority of the genes from the bin. The scaffolds then differ between the metagenomes but I guess the results would still be comparable. Anne

christophertbrown commented 6 years ago

Hi Anne,

That sounds reasonable. You will just want to be sure that your genomes for each sample satisfy the minimum requirements for iRep.

Chris

On Jun 5, 2018, at 11:08 PM, annekup notifications@github.com wrote:

Hi Chris, thanks for your reply. I want to compare several metagenomes and have individual assemblies for each of them. Thus I could take the scaffolds from the individual assemblies that contain a majority of the genes from the bin. The scaffolds then differ between the metagenomes but I guess the results would still be comparable. Anne

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