User: deni.ribicic

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Posts by deni.ribicic

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Comment: C: Metagenome bin sequence alignement
... Thanks a lot! Actually I have done that with CheckM, but CheckM places bins in a reference genome tree which is huge and not really suitable for plotting. Here kicks in my bioinformatics limitation, probably there is a way to prune it, which I am not aware of. I have a feeling that I am now spamming ...
written 11 weeks ago by deni.ribicic0
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Comment: C: Metagenome bin sequence alignement
... Thanks, got you. Now, more of a technical question. Say, I have a .fa file from a single bin containing sequences of single copy genes separated by headers containing genes names. Do you remove all headers in order to merge the sequences and name it with a single header containing bin name so you c ...
written 11 weeks ago by deni.ribicic0
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Comment: C: Deseq2: Time series experiment with 2 conditions and 5 time points
... I guess you misunderstood what I tried to say, or I haven't explain myself well. Basically I want to test whether there is difference in my microbial community composition between different treatments in a time-series. So i have oil incubation over the period of 64 days. I have sampled at day 0, 3, ...
written 11 weeks ago by deni.ribicic0
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Comment: C: Metagenome bin sequence alignement
... Thanks for the quick reply, I did already the prediction. When you saying marker genes, are you referring to the single copy genes that are used to evaluate bin completeness and contamination? Or are those genes phylogenetic specific genes? Thanks again. Deni ...
written 11 weeks ago by deni.ribicic0
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Metagenome bin sequence alignement
... Hi guys, I was wondering what is the best approach to make sequence alignment of reconstructed metagenomic bins in order to make phylogenetic tree? What I have now is fasta file for each bin containing a lot of contigs. Do I have to find and extract specific genes to perform alignment? If so, what ...
alignment bin tree written 11 weeks ago by deni.ribicic0 • updated 11 weeks ago by yzzhang30
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Comment: C: Available pipelines for functional annotaiton (COG, KEGG, GO) of genomes
... I realize this was posted some while ago, but it would be nice to have your opinion on the following matter. So, I did annotation of my metagenomes using PROKKA. Is it a valid approach to use PROKKA annotated ECs and convert them to GO terms just by matching it against ec2go list? Thanks, Deni ...
written 11 weeks ago by deni.ribicic0
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Answer: A: Deseq2: Time series experiment with 2 conditions and 5 time points
... Hi Stan, This is a bit late reply, but I am facing actually the same problem. So the answer is basically to separate your time-points and test each and every on certain condition? This seems to be tedious especially if you have a lot of time points! Cheers, Deni ...
written 4 months ago by deni.ribicic0
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Comment: C: Metagenomic shotgun sequence analysis- optimal approach
... Hi dago, Thanks for the reply. Actually I am interested in specific genes (i.e. hydrocarbon degrading genes). Now if I want to calculate taxa contribution to those genes how would you do it if not binning first? What I understand is that by creating bins you are gathering potential genes belongin ...
written 7 months ago by deni.ribicic0
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Metagenomic shotgun sequence analysis- optimal approach
... Hi Folks, I am relatively new to bioinformatics world, therefore having some issues to construct a workflow that would suit my needs. Hence, I would kindly ask for your opinion and advice. I have Illumina shotgun sequences of 5 metagenomes. I would like to end up with functional profile of all 5 sa ...
metagenomics workflow shotgun written 7 months ago by deni.ribicic0 • updated 7 months ago by dago2.2k

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