User: Thind amarinder
Thind amarinder • 120
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Posts by Thind amarinder
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... 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 ...
written 8 days ago by
Thind amarinder • 120
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... 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 amarinder • 120
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... 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 amarinder • 120
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... 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 amarinder • 120
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... 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 ...
written 3 months ago by
Thind amarinder • 120
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... 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 amarinder • 120
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... What if the publication has a color figure? ...
written 3 months ago by
Thind amarinder • 120
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... 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 amarinder • 120
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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 amarinder • 120
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... Where do we suppose to mention the version of the genome reference hg19/hg38 etc? ...
written 4 months ago by
Thind amarinder • 120
Latest awards to Thind amarinder
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4 months ago,
created a post with more than 5 votes.
For RNASeq tutorial for gene differential expression analysis
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5 months 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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voted at least 25 times.
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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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