Moderator: cpad0112

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cpad011212k
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Posts by cpad0112

<prev • 2,047 results • page 1 of 205 • next >
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Comment: C: Transforming MEGAN output with Krona
... `Was updateTaxonomy.sh run?` ...
written 9 hours ago by cpad011212k
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Comment: C: filtering out lines (rows) based on repeated zero values with awk in linux
... To make sure that 0 in gene names is not counted, I added gene10 entry copying gene 9 values and changing gene9 to gene 10. $ awk 'NR==1 {print}; NR !=1 {print $1, $1="", $0, gsub(/0/, "")}' file.txt | awk -v OFS="\t" 'NR==1 {print};NR!=1 && $NF<7 {NF--;print}' id sample1 sample ...
written 3 days ago by cpad011212k
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Comment: C: Vegetable databases usage
... Do you have a list of target species and know if the genomes are available? If you have a list of vegetables with genomes available, you can index the genomes and use fastqscreen for initial contamination screen. You can also use any target genome indices and run against fastqscreen to know the cont ...
written 8 days ago by cpad011212k
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Comment: C: Demovir: Taxonomic Classification of Viral Particle
... Please read the manual. Download the reference files, format them and keep them in correct place. ...
written 13 days ago by cpad011212k
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Comment: C: R ggplot2 -
... Do you want it this way? if so, please replace `Gene_name` with `chr` (reorder(Chr, row)). If you want same plot (as in OP), but for each chromosome separate, do a facet wrap: `facet_wrap( ~ Chr, ncol = length(unique(testDE$Chr)), scales = "free")`. This would plot X and Y axis on free scale. H ...
written 13 days ago by cpad011212k
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Comment: C: Is there a tool for calculating the number of uniquely mapped reads, ambigiously
... use combination of samtools and broad institute's website for flags ...
written 16 days ago by cpad011212k
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Comment: C: How to concatenate four fastq files of NextSeq in linux?
... https://www.biostars.org/u/61373/ @ I am not sure if that is the way I would handle. Most of the aligners, for a given sample, allow the user to furnish multiple read files and use them in alignment to produce one single alignment file (SAM/BAM), followed by quantification per sample. But every one ...
written 22 days ago by cpad011212k
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Comment: C: How to concatenate four fastq files of NextSeq in linux?
... if you are a cat person, use `cat` in *nix and if you are a reptile person, use [`merge_fastq` library](https://pypi.org/project/merge-fastq/). ...
written 23 days ago by cpad011212k • updated 22 days ago by RamRS25k
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Comment: C: annotated XY plot (volcano plot) with glimma
... can you do some thing like this? (replace df with de.df and assumption is that Ensembl IDs are row names of the data frame): ga2=data.frame(GeneID=df$genes, row.names=row.names(df)) glXYPlot(df$logFC,-log10(df$FDR), xlab="logFC", ylab="-log(FDR)", stat ...
written 24 days ago by cpad011212k
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Comment: C: How to get GTF file for Rousettus_aegyptiacus?
... This is incorrect. Link is about reference (fasta) downloading image. OP is about annotation (GTF/GFF3) file. ...
written 26 days ago by cpad011212k

Latest awards to cpad0112

Appreciated 16 days ago, created a post with more than 5 votes. For C: can someone read this result to me
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 4 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 5 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 3 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Problem installing Rgraphviz in R
Scholar 3 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 3 months ago, created an answer that has been accepted. For A: which feature is considered as expression level ?
Scholar 3 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 6 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 6 months ago, created an answer that has been accepted. For A: which feature is considered as expression level ?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Appreciated 8 months ago, created a post with more than 5 votes. For C: Remove columns and rows which have only NAs without deleting all the data
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change

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