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User: lokraj2003

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lokraj2003 • 80
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lokraj
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Posts by lokraj2003

<prev • 39 results • page 1 of 4 • next >
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Comment: C: Multiple test correction in Hyphy Analysis ?
... Thanks Brice. I did not split the genome. So, 1250 amino acids was one gene. So, I don't need to adjust my p -value ? Just to confirm I understood your point correctly. ...
written 5 months ago by lokraj2003 • 80
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Multiple test correction in Hyphy Analysis ?
... I did selection pressure analysis on viral genomes using MEME, SLAC and FUBAR on Datamonkey server. I am using p value < 0.05 for MEME and SLAC. Do I have to do any type of multiple test correction on the p-value given by MEME and SLAC ? How can I do Bonferroni Test if I have 85 sequences each wi ...
hyphy selection pressure datamonkey bonferroni written 5 months ago by lokraj2003 • 80 • updated 5 months ago by Brice Sarver • 3.5k
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Comment: C: Nucleotide to amino acid conversion of multiple sequences
... Actually it works, but then parsing output became tedious. Thinking of a way to parse the output. ...
written 7 months ago by lokraj2003 • 80
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Comment: C: Nucleotide to amino acid conversion of multiple sequences
... I am going to do selection pressure analysis. So, I will have to do multiple sequence alignment before I could actually do selection pressure analysis. ...
written 7 months ago by lokraj2003 • 80
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Nucleotide to amino acid conversion of multiple sequences
... I have 220 nucleotide sequences. They are around 7000 bp and each of them should translate into one protein of around 2100 amino acids. There are some functions already available in R that can convert nucleotide sequence to amino acid sequence. But, these available functions like `Translate` in `seq ...
biocondutor bippyton protein dna written 7 months ago by lokraj2003 • 80 • updated 7 months ago by Mensur Dlakic • 3.6k
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Creating SingleCellExperiment class from scratch !
... I am trying to learn single cell RNA-Seq data analysis. Right now I am following Seurat and Monocle documentation. I am aware of the fact that we have to create a single cell experiment object, which basically acts as a container for the scRNA data. But, I want make one these container from scratch ...
bioconductor monocle scrna seurat written 8 months ago by lokraj2003 • 80
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Extracting promoter sequence with GenomicFeatures ?
... I am trying to extract promoter sequence of a non-model organism (Orf virus). I used flank function from GenomicFeatures to extract 50 base pairs upstream of start codon. promoters <- flank(gr, 100) Then I used those coordinates on the costum BSgenome Orf virus genome package that I made by ...
bioconductor genomicfeatures written 9 months ago by lokraj2003 • 80
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Comment: C: Creating taxonomic database using GFF3 file ?
... Thank you ! It worked. ...
written 9 months ago by lokraj2003 • 80
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Creating taxonomic database using GFF3 file ?
... I am trying to create a taxonomic database using GenomicFeatures package. I downloaded GFF3 file from the NCBI. Codes : orf <- GenomicFeatures::makeTxDbFromGFF("orf.gff3",format="auto") I get following output : Orf TxDb object: Db type: TxDb Supporting pack ...
bioconductor genomefeatures written 9 months ago by lokraj2003 • 80 • updated 9 months ago by SMK • 1.9k
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Consensus sequence from SAM or BAM file?
... I am trying to perform reference-based assembly. Most of the tutorials teach how to create a bam file and view alignemnts in IGV or Tablet. But, I want a assembled genome sequence in fasta format. How can I do that ? Is there any tool or linux syntax available for this purpose ? ...
assembly written 10 months ago by lokraj2003 • 80

Latest awards to lokraj2003

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Making row and column names visible on heatmap.
Popular Question 10 weeks ago, created a question with more than 1,000 views. For qPCR Ct value to the genome copy number
Popular Question 4 months ago, created a question with more than 1,000 views. For How to create a nexus file for BEAST ?
Popular Question 4 months ago, created a question with more than 1,000 views. For qPCR Ct value to the genome copy number
Popular Question 9 months ago, created a question with more than 1,000 views. For qPCR Ct value to the genome copy number
Popular Question 9 months ago, created a question with more than 1,000 views. For Annotation with Prokka or RAST.
Scholar 10 months ago, created an answer that has been accepted. For A: how to appropriately export datasets from R studio in an appropriate style?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: how to appropriately export datasets from R studio in an appropriate style?
Popular Question 11 months ago, created a question with more than 1,000 views. For How to plot heatmap for the matrix for the pairwise comparison of sequence similarity in R ?
Popular Question 13 months ago, created a question with more than 1,000 views. For Annotation with Prokka or RAST.
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