Moderator: cpad0112
cpad0112 ♦ 12k
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Posts by cpad0112
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... `Was updateTaxonomy.sh run?` ...
written 9 hours ago by
cpad0112 ♦ 12k
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... 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 && $NF<7 {NF--;print}'
id sample1 sample ...
written 3 days ago by
cpad0112 ♦ 12k
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Comment:
C: Vegetable databases usage
... Do you have a list of target species and know if the genomes are available? If you have a list of vegetables with genomes available, you can index the genomes and use fastqscreen for initial contamination screen. You can also use any target genome indices and run against fastqscreen to know the cont ...
written 8 days ago by
cpad0112 ♦ 12k
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... Please read the manual. Download the reference files, format them and keep them in correct place. ...
written 13 days ago by
cpad0112 ♦ 12k
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Comment:
C: R ggplot2 -
... Do you want it this way?
if so, please replace `Gene_name` with `chr` (reorder(Chr, row)).
If you want same plot (as in OP), but for each chromosome separate, do a facet wrap: `facet_wrap( ~ Chr, ncol = length(unique(testDE$Chr)), scales = "free")`. This would plot X and Y axis on free scale. H ...
written 13 days ago by
cpad0112 ♦ 12k
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... use combination of samtools and broad institute's website for flags ...
written 16 days ago by
cpad0112 ♦ 12k
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... 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
cpad0112 ♦ 12k
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... 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/). ...
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... 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
cpad0112 ♦ 12k
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... This is incorrect. Link is about reference (fasta) downloading image. OP is about annotation (GTF/GFF3) file. ...
written 26 days ago by
cpad0112 ♦ 12k
Latest awards to cpad0112
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For C: can someone read this result to me
Teacher
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For A: convert SNP calls to amino acid change
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For A: .fai file generation for a vcf file containing snps
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For A: convert SNP calls to amino acid change
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For A: convert SNP calls to amino acid change
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For A: convert SNP calls to amino acid change
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For A: .fai file generation for a vcf file containing snps
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For C: Problem installing Rgraphviz in R
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For A: which feature is considered as expression level ?
Scholar
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For A: .fai file generation for a vcf file containing snps
Teacher
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For A: convert SNP calls to amino acid change
Teacher
3 months ago,
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For A: convert SNP calls to amino acid change
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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
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6 months ago,
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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
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For C: Remove columns and rows which have only NAs without deleting all the data
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8 months ago,
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For A: convert SNP calls to amino acid change
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