User: ashish

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ashish570
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Posts by ashish

<prev • 170 results • page 1 of 17 • next >
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Comment: C: How to identify which genes are responsible for the different cluster without P
... Is there a specific reason why you do not want to do PCA, it sounds like a good job for PCA. You can also visualize loadings plot using [PCATools][1] package. It is pretty easy to make [1]: https://bioconductor.org/packages/release/bioc/vignettes/PCAtools/inst/doc/PCAtools.html ...
written 12 days ago by ashish570
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Comment: C: Issue installing rmats using conda
... I have rmats installed in a separate environment and it uses python 3.7. ...
written 16 days ago by ashish570
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Comment: C: Issue installing rmats using conda
... Make a separate environment and install rmats in it. Avoiding these conflicts by making separate environments is the whole point of using conda. ...
written 16 days ago by ashish570
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Comment: C: DESeq2 and DEXSeq
... There are no programs which can incorporate both deseq and dexseq according to my knowledge. However, if you are interested in splicing I would suggest junctionseq instead of dexseq. ...
written 16 days ago by ashish570
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Comment: C: DESeq2 and DEXSeq
... DESeq2 is for differential gene expression and DEXSeq is for differential exon usage. Both are different things. What is your aim here? ...
written 19 days ago by ashish570
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Comment: C: How to a make schematic picture for RNA-seq steps
... I cannot see the picture but if you want to do this in R then use the package diagrammeR. [Here][1] is a short tutorial to get you started. [1]: https://datascienceplus.com/how-to-build-a-simple-flowchart-with-r-diagrammer-package/ ...
written 23 days ago by ashish570
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Comment: C: Finding common and different genes between species
... Are these plants related? You may look at presence/absence variation tools. These are part of pangenome/transcriptome analysis methods. Here is one [approach][1]. [1]: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6174-3 ...
written 9 weeks ago by ashish570
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Comment: C: calculating fold change
... How did you get this list of differentially expressed genes? ...
written 10 weeks ago by ashish570
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Answer: C: Downloading gene sequences for a list of genes using E-utilities
... Most probably these are ids from Oryza sativa indica which is a different sub-species than the one we see more often (japonica). It was sequenced by BGI, China and the assembly is [available][1] at ensembl plants which can be accessed using biomart. However, BGI has sequenced many other plants and w ...
written 10 weeks ago by ashish570
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Comment: C: Downloading gene sequences for a list of genes using E-utilities
... Have you tried biomart at ensembl plants? I was able to download gene sequences of the ids you provided by choosing Oryza sativa indica group as the plant. Biomart can also be accessed in R if you want to put this inside a script. ...
written 10 weeks ago by ashish570

Latest awards to ashish

Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Avoid repetition in script
Popular Question 4 months ago, created a question with more than 1,000 views. For infer sub-families from phylogenetic tree
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: How to convert .tar file to fasta file?
Popular Question 6 months ago, created a question with more than 1,000 views. For orthologue mapping using circos
Popular Question 7 months ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Popular Question 7 months ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Great Question 7 months ago, created a question with more than 5,000 views. For retrieving best hit in local blast output
Great Question 10 months ago, created a question with more than 5,000 views. For heatmap using FPKM values
Great Question 11 months ago, created a question with more than 5,000 views. For levels in gene ontology
Centurion 11 months ago, created 100 posts.
Voter 13 months ago, voted more than 100 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Popular Question 21 months ago, created a question with more than 1,000 views. For Gap treatment in MEGA for ML phylogeny
Popular Question 21 months ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 21 months ago, created a question with more than 1,000 views. For blastn for very short sequences
Popular Question 2.1 years ago, created a question with more than 1,000 views. For blastn for very short sequences
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 2.1 years ago, created a question with more than 1,000 views. For retrieving best hit in local blast output
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 2.5 years ago, created a question with more than 1,000 views. For retrieving best hit in local blast output
Popular Question 2.7 years ago, created a question with more than 1,000 views. For how to analyse gene expression using RNA-seq data
Popular Question 2.7 years ago, created a question with more than 1,000 views. For how to analyse gene expression using RNA-seq data
Popular Question 2.9 years ago, created a question with more than 1,000 views. For heatmap using FPKM values
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