User: Leandro de Mattos

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60
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Location:
Brazil
Website:
http://lambaribioinfot...
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4 months ago
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2 years, 10 months ago
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Posts by Leandro de Mattos

<prev • 28 results • page 1 of 3 • next >
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Comment: A: Hotspot file to Ion torrent
... Dear Titus, the panel is already designed. I want to do known annotation file, with mutations known in the amplicons, not the panel amplicons design: Partial example of a HotSpots BED file below: track name="HSMv12.1" description="AmpliSeq Pool HSMv12.1" type=bedDetail chr1 43815007 ...
written 4 months ago by Leandro de Mattos60 • updated 4 months ago by genomax33k
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Hotspot file to Ion torrent
... Dear Someone already created a Hostpot file (annotation) for use in Ion torrent, is there any "easy" way to do this ? I would like to use the database Clinvar, Cosmic and others. Every help is welcome. Thank in advance. ...
hotspot annotation snps written 4 months ago by Leandro de Mattos60
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Answer: A: Heatmap of diferent conditions
... Dear, I managed to do the figure, sharing : > data <- read.csv2(file="result.csv", sep=";", dec=";") > data rnames > data[,1] rnames data <- read.csv2(file="result.csv", sep=";", dec=",") > data mat_data <- data.matrix(data[,2:ncol(data)]) mat_data > rownames(mat_data) < ...
written 15 months ago by Leandro de Mattos60
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Comment: A: Heatmap of diferent conditions
... For example, in R: x <- read.table("fitness.csv",sep=",", fill = TRUE) x_matrix<-data.matrix(x) row.names(x) x_heatmap <-heatmap(x_matrix,col = cm.colors(256), scale="column") But is not ok yet; ...
written 16 months ago by Leandro de Mattos60
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Heatmap of diferent conditions
... Dear, How can I make a heatmap of these data (Table)? Sample Conditions GrowthX GrowthY GrowthZ GrowthW 2ugAg+ Metal -3.085.361 15.085.361 -15.085.361 15.785.361 2ugAg+ Metal -3.005.842 13.005.842 -13.005.842 13.705.842 2ugAg+ Metal -2.997.751 11.996.551 -11.996.551 11.796.551 1ugZn+ Metal -2.890. ...
fitness score heatmap written 16 months ago by Leandro de Mattos60
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identification and to comparison of the List of ECs of a specific metabolic pathway
... I would like to suggestions of bioinformatics tools or scripts of how to get all genes / EC of a specifc metabolic pathway (automatically) of the KEGG and compare between different organisms the presence / absence of these genes. Thanks for any suggestion, Leandro ...
kegg written 16 months ago by Leandro de Mattos60
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Put taxonomy code abreviattion in biom table
... Dear all, I want to help, if possible How do I change the taxonomy using cut (shell), awk and seed: my actual taxonomy, has no abbreviation code on the begin, I would like to put the code (d: domain, p: phylum, etc) in each taxonomy level, For exempl   I have: Eukaryota;__Opisthokonta;__Metazoa; ...
awk qiime silva database written 23 months ago by Leandro de Mattos60 • updated 22 months ago by Biostar ♦♦ 20
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Answer: A: Problem: kmergenie has a minimum number of input of reads?
... Hi Hian, but I used only one input, I have one file. ...
written 2.6 years ago by Leandro de Mattos60
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Answer: A: Problem: kmergenie has a minimum number of input of reads?
... Dear Rayan, I used : ./kmergenie *.csfasta Operating systems: Biolinux (last version) I have installed the R and python. ...
written 2.6 years ago by Leandro de Mattos60
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Problem: kmergenie has a minimum number of input of reads?
... Hi all, I'm the following problem with kmergenie: Warning! using max number of read files (2000) error opening file: # fitting model to histograms to estimate best k could not predict a best k value Execution of decide failed (return code 0) How can I increase the read number of input?? Other que ...
kmergenie k-mers written 2.6 years ago by Leandro de Mattos60

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Popular Question 12 months ago, created a question with more than 1,000 views. For Low percentage of reads in Tophat, Is the any setting to improve?
Popular Question 23 months ago, created a question with more than 1,000 views. For Low percentage of reads in Tophat, Is the any setting to improve?

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