User: Thind amarinder

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Posts by Thind amarinder

<prev • 65 results • page 1 of 7 • next >
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Adjustment of number of mutations of 3'UTR region for UTR length
... For mutational study in 3' UTR regions of the genes, I would like to find out which 3' UTR are highly mutated as compared to others. But of course, the original number is biased because of the factors such as length. I know there are tools (mutsigcv, mutpanning etc) that correct mutational backgroun ...
genome sequence utr snv rna-seq written 8 days ago by Thind amarinder120
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Answer: A: Are there any tutorials available for Nanostring data differential expression an
... One GitHub repository, but not Documented well. [https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa163/5891144][1] I am working on it and modifying/writing some R script for Deseq2. When done I will share it on Github and update it here. If you have technical replicate Better to go ...
written 17 days ago by Thind amarinder120
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Answer: A: Inferring genotype based on RNA sequences (RNA-seq variant calling)
... Integrated analyses can give more insights such as "SNPs resulting from post-transcriptional modifications". explained in this article [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216838][1] ***SNPs resulting from post-transcriptional modifications, such as RNA editing, whic ...
written 11 weeks ago by Thind amarinder120
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Comment: C: Best Way To Measure Mirna-Seq Abundance
... I don't think it is a unique question and so new one usually ends up with penalties or with a comment of someone that "it is asked somewhere before". However, here is it [https://www.biostars.org/p/476599/][1] [1]: https://www.biostars.org/p/476599/ ...
written 3 months ago by Thind amarinder120
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interaction prediction of circRNA and miRNA and co -expression network
... I want to predict circular RNAs - miRNAs interactions. I am interested in collecting/extracting this information from available resources and/or performing co-expression network analyses. The issues/challenges that I am facing are (1) Universal annotation of circular RNA? I don't know if it exists ...
ngs mirna circrna rna-seq coexpression written 3 months ago by Thind amarinder120
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Comment: C: Best Way To Measure Mirna-Seq Abundance
... I would like to use miRNA abundance for co-expression analyses, I am thinking of using count per million (CPM)? Do you have any feedback or suggestions for this? thanks ...
written 3 months ago by Thind amarinder120
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Comment: C: Bioinformatics Journal with no publishing fees?
... What if the publication has a color figure? ...
written 3 months ago by Thind amarinder120
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Answer: A: Potential Bacteria Contamination - RNA-Seq
... Decotaminer tool investigates the origin of unmapped reads and assigns taxon. DecontaMiner, a tool to unravel the presence of contaminating sequences among the unmapped reads. [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2684-x][1] [https://github.com/amarinderthind/de ...
written 3 months ago by Thind amarinder120
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Comment: C: Gene list from bed file
... I tried this and I would like to add something extra. Also select Track:- UCSC. I obtained multiple lines w.r.t. original co-ordinates in .bed so I collapsed it using bedtools: `bedtools map -a original.bed -b ucsc_based_gene_list.bed -c 5 -o collapse` ...
written 4 months ago by Thind amarinder120
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Comment: C: To Get All Genes Within A Genomic Region
... Where do we suppose to mention the version of the genome reference hg19/hg38 etc? ...
written 4 months ago by Thind amarinder120

Latest awards to Thind amarinder

Appreciated 4 months ago, created a post with more than 5 votes. For RNASeq tutorial for gene differential expression analysis
Popular Question 5 months ago, created a question with more than 1,000 views. For Not able to retrieve PDB id from standalone blast against PDB
Supporter 5 months ago, voted at least 25 times.
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Not able to retrieve PDB id from standalone blast against PDB

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