User: ashish

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ashish480
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Posts by ashish

<prev • 155 results • page 1 of 16 • next >
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Answer: A: Using DESeq2 for time-series analysis
... You are right in using LRT to find DE genes, in the results ignore the log2FC column and use a stringent adjusted pvalue cutoff to get a reasonable number of genes for downstream analysis. However, as Asaf has said your design seems to be wrong, shouldn't you be comparing `~time` with `~1`. There ...
written 28 days ago by ashish480
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Comment: C: Avoid repetition in script
... [Writing `for` loops in R][1] [Important tip for using ggplot in a `for` loop][2] Also look at the `*apply` family of functions in R, they are sometimes faster and easier to use then writing a loop. [1]: https://r4ds.had.co.nz/iteration.html [2]: https://stackoverflow.com/questions/15678261/ ...
written 5 weeks ago by ashish480
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Answer: A: How to visualise KEGG pathway?
... [KEGG color pathway][1] is exactly for this purpose. It will give one pathway map for each of your samples. If you have only 2-3 samples you can show all of them in one pathway map using [pathview][2]. [1]: https://www.genome.jp/kegg/tool/map_pathway3.html [2]: https://www.bioconductor.org/pac ...
written 7 weeks ago by ashish480
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Answer: A: Plot biological process of DAVID analysis in a barplot
... This is a barplot and can be made easily in R using ggplot. First remove all the unnecessary columns in the DAVID output file. Just keep the GO terms and their associated pvalue. Assuming you can get the data in a three column format where first column is GO term, second is module name and third is ...
written 3 months ago by ashish480
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Comment: C: salmon output to linear models in R
... Just melt the matrix in long format and do `lm` using `tpm ~ dose + variety` or `tpm ~ dose + variety + dose:variety` (will also check for interaction effects). ...
written 3 months ago by ashish480
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Comment: C: Why NB distribution is preferred in RNA-Seq while normal distribution is preferr
... Just to add to the answer. Sleuth assumes log abundances are normally distributed. ...
written 3 months ago by ashish480
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Comment: C: RNA-seq of 3'-UTRs
... I was wrong above in suggesting to use the unmasked genome. See [this][1]. STAR does not discriminate between soft-masked (lowercase) or unmasked genome, I am not sure about other aligners. So it should not create any differences. [1]: https://groups.google.com/forum/#!topic/rna-star/2wdHXaPv_v ...
written 3 months ago by ashish480
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Comment: C: RNA-seq of 3'-UTRs
... You have already used the whole genome for alignment but you used Mus_musculus.GRCm38.dna_sm.primary_assembly.fa which is soft masked genome assembly, If there is no particular reason to use masked assembly you should use Mus_musculus.GRCm38.dna.primary_assembly.fa which has no masking. There are s ...
written 3 months ago by ashish480
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Comment: C: RNA-seq of 3'-UTRs
... What downstream application did you use and what was the error it produced ? cDNA would also contain 5'-UTR and coding regions. I think it would be better to extract the 3'-UTR regions from the genome using the gtf file and run salmon on them to count the reads mapping to these 3'-UTRs. You can als ...
written 3 months ago by ashish480
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Answer: C: How to convert .tar file to fasta file?
... This is a readymade index, you can uncompress and directly use it for read alignment. If you want to generate the original genome used for creating this index use `hisat2-inspect` but its not required. ...
written 3 months ago by ashish480

Latest awards to ashish

Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Avoid repetition in script
Popular Question 10 weeks ago, created a question with more than 1,000 views. For infer sub-families from phylogenetic tree
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: How to convert .tar file to fasta file?
Popular Question 4 months ago, created a question with more than 1,000 views. For orthologue mapping using circos
Popular Question 4 months ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Popular Question 4 months ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Great Question 5 months ago, created a question with more than 5,000 views. For retrieving best hit in local blast output
Great Question 8 months ago, created a question with more than 5,000 views. For heatmap using FPKM values
Great Question 8 months ago, created a question with more than 5,000 views. For levels in gene ontology
Centurion 9 months ago, created 100 posts.
Voter 10 months ago, voted more than 100 times.
Popular Question 18 months ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Popular Question 18 months ago, created a question with more than 1,000 views. For Gap treatment in MEGA for ML phylogeny
Popular Question 18 months ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 18 months ago, created a question with more than 1,000 views. For blastn for very short sequences
Popular Question 22 months ago, created a question with more than 1,000 views. For blastn for very short sequences
Popular Question 22 months ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 22 months ago, created a question with more than 1,000 views. For retrieving best hit in local blast output
Popular Question 23 months 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 Problem building reference genome using STAR
Popular Question 2.3 years ago, created a question with more than 1,000 views. For retrieving best hit in local blast output
Popular Question 2.4 years ago, created a question with more than 1,000 views. For how to analyse gene expression using RNA-seq data
Popular Question 2.5 years ago, created a question with more than 1,000 views. For how to analyse gene expression using RNA-seq data
Popular Question 2.6 years ago, created a question with more than 1,000 views. For heatmap using FPKM values
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