User: thjnant

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thjnant100
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Posts by thjnant

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Comment: C: DESeq2 for pairwise comparison of multiple groups
... So sorry for cross-posting. I mentioned it in my post in bioconductor forum. I will now add it to my question here too. ...
written 15 days ago by thjnant100
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Comment: C: DESeq2 for pairwise comparison of multiple groups
... Thank you for your reply. I checked the results between the two. Of the top 50 most significant comparisons, 27 genes are common. I have more significant genes detected when I use a dataset containing only the pair of interest. out of 13297 with nonzero total read count adjusted p-value < ...
written 15 days ago by thjnant100
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DESeq2 for pairwise comparison of multiple groups
... Hello, I have 4 different groups (species) that I want to look into their differential gene expression. I call them A, B, C and D. I have 5 - 8 replicates for each group and I am using DESEQ2 for the analysis. I am facing a difficulty which I cannot interpret. I first made a separate data frame ...
R deseq2 rna-seq written 15 days ago by thjnant100
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Comment: C: High logfold change but padj > 0.1 in DESEQ2
... Extremely helpful, thank you so much! ...
written 5 weeks ago by thjnant100
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High logfold change but padj > 0.1 in DESEQ2
... Hello, I am analysing RNA-seq data to investigate differential gene expression in hybrids compared to parental species. Since I work with natural populations, I have few samples (5 of two different tissues for each species and hybrid). I am using the DESEQ2 package for my expression analysis. What ...
R deseq2 rna-seq expression written 5 weeks ago by thjnant100 • updated 5 weeks ago by ATpoint35k
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de-novo RNA assembly and assembly of aligned RNA-seq reads
... I am reading the great review paper by Yandel et al 2012 on Genome annotation. I came across the final paragraph: "They (RNA-seq data) can be assembled de novo — that is, independently of the genome — using tools such as ABySS, SOAPdenovo and Trinity; the resulting transcripts are then realigned to ...
rna-seq written 4 months ago by thjnant100
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Comment: C: Learn perl or python for bioinformatics?
... Thanks a lot! ...
written 4.9 years ago by thjnant100
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(Closed) Learn perl or python for bioinformatics?
... Hello, I know this is a repeated question but I would like to have new opinions on it as time changes preferences. I am about to finish the first year of my PhD studies in evolutionary genetics. I have a biology background. During this first year, I have tried to learn a bit of everything, from C t ...
perl python written 4.9 years ago by thjnant100 • updated 4.9 years ago by mxs530
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Comment: C: SNP calling from pooled RNA-seq data
... Oh, yes, you are right. As one allele may not be expressed, so, then the truly heterozygote position will be called as a homozygote. Well, I should handle the limitations. Thanks again. ...
written 5.4 years ago by thjnant100
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Comment: C: SNP calling from pooled RNA-seq data
... Thanks for your comment. From individually sequenced RNA-seq data is possible to see whether an individual is homozygote or heterozygote for a given position especially one can always check the bam files against the reference. But as you said, knowing whether a position is homozygote or heterozygote ...
written 5.4 years ago by thjnant100

Latest awards to thjnant

Student 12 weeks ago, asked a question with at least 3 up-votes. For Ancestral allele in VCF files
Great Question 4.9 years ago, created a question with more than 5,000 views. For MAF option in vcftools
Great Question 4.9 years ago, created a question with more than 5,000 views. For Converting gtf format to bed format
Great Question 4.9 years ago, created a question with more than 5,000 views. For Problem with blastp when blasting against custom made database
Epic Question 4.9 years ago, created a question with more than 10,000 views. For Converting gtf format to bed format
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Learn perl or python for bioinformatics?
Popular Question 4.9 years ago, created a question with more than 1,000 views. For SNP calling from pooled RNA-seq data
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Convert Illumina 1.5 to Illumina 1.8
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Masking reference for RNA-seq alignments
Popular Question 4.9 years ago, created a question with more than 1,000 views. For SNP calling from pooled RNA-seq data
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Correlation Between Alleles
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Fst Across Several Population
Popular Question 4.9 years ago, created a question with more than 1,000 views. For MAF option in vcftools
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Ancestral allele in VCF files
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Plotting Fst
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Error with database alias when running blastp
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Converting gtf format to bed format
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Problem with blastp when blasting against custom made database
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Weir And Cockerham Fst
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Popular Question 4.9 years ago, created a question with more than 1,000 views. For Investigating a genome assembly
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Popular Question 4.9 years ago, created a question with more than 1,000 views. For STAR_2PASS for SNP calling from RNA seq data
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Popular Question 4.9 years ago, created a question with more than 1,000 views. For Aligning fasta sequences against a reference genome with scaffolds

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