User: O.rka

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O.rka50
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Posts by O.rka

<prev • 55 results • page 1 of 6 • next >
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Why does clustalo guidetree have negative values for branch lengths?
... **What does it mean when clustal omega has negative values in the guidetree?** Below is a snippet: ( Otu000011:0.0158103 , Otu000082:0.0158103 ):0 , Otu000264:0.0158103 ):0.00296443 ):0.00790514 ):-0.00469368 ):-0.000741107 ):0.000401434 ):-0.00 ...
clustalo clustal alignment tree written 6 days ago by O.rka50
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How associate raw reads with MetaCyc/Taxonomy from HUMAnN2?
... Extending a discussion: https://groups.google.com/forum/#!msg/humann-users/0rbswpcxL1M/4mZNbNd8DAAJ According to the conversation above this is what appears to be going on, PLEASE CORRECT WHERE NECESSARY: 1. Reads would be mapped to genes in the following files in the [name]_temp/ directory: 1a. [ ...
metacyc humann transcriptomics humann2 written 12 days ago by O.rka50
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Comment: A: Which method is good for getting logFC for pairwise comparsion of replicates?
... Any progress on this? I'm running the metrics on a bunch of distances measures right now to see the best one for my data set. ...
written 3 months ago by O.rka50
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Find list, flatfiles, or database of all gram + or - bacteria?
... I have an OTU table and I want to see all of the gram - and gram + bacteria in the communities. Is there a list that has all of the gram + or gram - bacteria anywhere? Preferably the genera and whether or not they are gram + or - in a table format. I am comfortable webscraping if there is a resour ...
taxonomy written 4 months ago by O.rka50
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Comment: C: How to merge quality trimmed interlaced reads?
... Thank you. I think I may have had some fundamental information incorrect about paired end sequencing technology. I was under the impression that you have overlapped segments so if you had 75 bp reads you would end up with ~150 bp reads. It seems like that is not the case. So for paired end reads ...
written 4 months ago by O.rka50
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How to merge quality trimmed interlaced reads?
... I have paired end reads from Illumina NextSeq. I've removed adapters/primers, quality trimmed, and interlaced the forward and reverse reads. I now have a single fasta (not fastq) file with the following structure: >NS500647:208:HYKFFBGX2:1:11101:9580:1154 1:N:0:GATCAG GTGGTCAGCAGACGT ...
rna-seq written 4 months ago by O.rka50
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What is the minimum number of non-ribosomal reads that can be used for E. coli transcriptomics?
... I have paired end Illumina NEXTSeq reads with 75 bp read-length with samples in ~triplicates (sometimes duplicates, sometimes I'll have 6). I was thinking 2 Million reads would be a good target and if there are a few replicates with high pearson correlation that have over 1 Million then that should ...
rna-seq written 4 months ago by O.rka50
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Is logFC in edgeR base e, 2, or 10?
... I am trying to find in the documentation of edgeR where it says the default base of the log function. I've used `exactTest` and `topTags` it gives me `logFC` but is it base `e`, `2`, or `10`? ...
differential bioconductor logfc edger written 5 months ago by O.rka50 • updated 5 months ago by Devon Ryan82k
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Comment: C: How to compare 2 separate coexpression networks each with the same genes?
... Interesting answers. I will take a look at the regression. However, at that point it wouldn't be correlation values? Also, if you get some extra time can you take a look at this question about `modulePreservation` https://support.bioconductor.org/p/106661/ ...
written 5 months ago by O.rka50
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Comment: C: How to compare 2 separate coexpression networks each with the same genes?
... Thanks for being helpful with all of those questions. I still need to look more into the details but it's a tool that I didn't even know existed. Really inspiring. ...
written 5 months ago by O.rka50

Latest awards to O.rka

Great Question 3 months ago, created a question with more than 5,000 views. For How to tell bloodtype from SNPs data?
Popular Question 4 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 8 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Supporter 16 months ago, voted at least 25 times.
Popular Question 18 months ago, created a question with more than 1,000 views. For How to tell bloodtype from SNPs data?
Student 2.0 years ago, asked a question with at least 3 up-votes. For Most up-to-date Gene Ontology [GO] analysis?

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