User: Leandro de Mattos

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70
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Location:
Brazil
Website:
http://lambaribioinfot...
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2 weeks, 6 days ago
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3 years ago
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Posts by Leandro de Mattos

<prev • 30 results • page 1 of 3 • next >
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PINDEL and somatic mutations
... For illumina I need to Recalibrated bases and Indelrealigned. I would like to known if Is necessary Recalibrated bases and Indelrealigned (GATK software) of bam (IonTorrent) for further Pindel Analysis?? Thanks, Leandro ...
gatk indelrealigned pindel written 25 days ago by Leandro de Mattos70
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pindel somatic indel filter
... I'm trying to use the script (https://github.com/genome/pindel/tree/master/somatic_filter/somatic_indelfilter.pl) perl /root/pindel/somatic_filter/somatic_indelfilter.pl somatic.indel.filter.config My result is informing that it has no reads, but is not trure, because the reads are there. The outpu ...
somatic_indelfilter.pl written 7 weeks ago by Leandro de Mattos70
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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 6 months ago by Leandro de Mattos70 • updated 6 months ago by genomax37k
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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 6 months ago by Leandro de Mattos70
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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 17 months ago by Leandro de Mattos70
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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 18 months ago by Leandro de Mattos70
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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 18 months ago by Leandro de Mattos70
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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 18 months ago by Leandro de Mattos70
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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 2.1 years ago by Leandro de Mattos70 • updated 2.0 years 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 2.7 years ago by Leandro de Mattos70

Latest awards to Leandro de Mattos

Popular Question 6 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 14 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 2.1 years 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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