User: dllopezr

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dllopezr40
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Posts by dllopezr

<prev • 32 results • page 1 of 4 • next >
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sorting columns by same values to do DEG analysis
... Hi community! I am working with metagenomic output from MG-RAST, but the columns don't match and I need to solve this before doing my DeSEQ analysis. The table is something like this GeneName Count GeneName Count GeneName Count GeneName Count GeneA x GeneB x GeneA x Ge ...
sorting columns differential expression written 8 weeks ago by dllopezr40 • updated 8 weeks ago by Fabio Marroni2.1k
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Comment: C: Mock Metagenome Gene Content
... Thanks for your Answer Nitin. The problem is that I don't want to find out the abundance of an organism, I want to count the abundance of some genes of interest. For example, how many time the gene "nifH" is present in the sample, for this purpose I need to know the organism that carry this gene, ho ...
written 11 weeks ago by dllopezr40
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Mock Metagenome Gene Content
... Hi, community! I need to work with a mock metagenome community for the optimization of the alignment parameters of a tool I've found this community: https://www.nature.com/articles/sdata201681, that is composed of 26 bacterial and archaeal genomes. For the purpose of my work I need to know the a ...
metagenome mock community gene content written 11 weeks ago by dllopezr40
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Filter by Tax Rank in Kegg API
... Hi, community! I am using the KEGG REST API to retrieve plain text files of some genes of interest. For example: `http://rest.kegg.jp/get/enzyme:1.18.6.1` to obtain all info of the enzyme 1.18.6.1, including the genes associated with, or `http://rest.kegg.jp/find/genes/nifh` to obtain a list o ...
rest api taxonomy kegg written 3 months ago by dllopezr40
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Cutadapt wrong behaviour
... Hi, community! I am using cutadapt v 1.18 in paired end mode to trim shotgun metagenomic sequences. My command line is the following: cutadapt -q 20,20 -m 70:70 -a "ADAPTER_FORWARD" -A "ADAPTER REVERSE" -o forwardoutput.fastq -p reverseoutput.fastq input_forward.fastq input_reverse.fastq -e 0. ...
cutadapt written 3 months ago by dllopezr40 • updated 3 months ago by gb590
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Comment: C: Change python version to run cutadapt
... Hi Kevin! I Tried the @finswimmer solution but a "permission" message appear. Tomorrow I will talk to my system administrator and I will try again. I will keep you notified. Regards! ...
written 3 months ago by dllopezr40
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Change python version to run cutadapt
... Hi everyone! I want to run cutadapt with a lot of shotgun sequences, but it takes to much time to run. Reading the documentation of this tool I found that multithreading is support but only when Python 3.3 or later is used. By default, my python version is 2.7 but I also have installed python 3.4. ...
python version cutadapt written 3 months ago by dllopezr40
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Overview questions about K-nearest neighbor classification methods
... Hi everyone! Suppose that you have a set of sequences that you belong to a gene, and also you have a set of sequences of unknow functions, and you want to know if some of this latter sequences belong to the gene of interest. Well..this is my problem. I am reading of sequence classification methods ...
k -nearest neighbor sequence classification written 3 months ago by dllopezr40 • updated 7 weeks ago by Biostar ♦♦ 20
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How to include complete labels names in R boxplot
... Hi everyone! I am doing an R BoxPlot of OTU abundance trough different samples, but the labels of the x axes are incomplete: For example, one sample name is T1P1_T2_C-1, but in the plot, the labels show only from the P letter. The code I am using is: boxplot(OTUs[, 2:13], main="Boxplot OTU' ...
boxplot R label written 4 months ago by dllopezr40 • updated 4 months ago by zx87546.5k
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Comment: C: Replace between character and white space using unix sed
... Hi @Kevin, thank you for your help! If you don't mind, could you explain to me how this command works, especially this part `ChrStart\-[0-9]*[[:blank:]]`? What I really want to do is to pass this numbers to different variables, say "ChrStart" = $1 and ChrStop = $2 to pass to another command. The ...
written 4 months ago by dllopezr40

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