User: arup

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arup1.4k
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India
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http://arupgsh.github.io/
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3 hours ago
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3 years, 7 months ago
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PhD student @ Institute of Life Science, Bhubaneswar

Posts by arup

<prev • 182 results • page 1 of 19 • next >
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Comment: C: Adding p-value to box plot
... Share an excerpt of the dataset and the code you are using. ...
written 6 days ago by arup1.4k
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Comment: C: Duplicate row name not allowed while reading the file in R
... Check the `row.names` column with `uniq -d` to see if any duplicate gene/transcript id present. ...
written 10 days ago by arup1.4k
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Comment: C: Demultiplexing single cell RNA-Seq data
... Can you share more details like platform used for the experiment and how you got the fastq files? ...
written 10 days ago by arup1.4k
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Comment: C: see reads in .bam file, no counts after HTseq
... I agree that Kallisto/Salmon can provide more accurate transcript quantification. But I was recommending featureCounts as it takes less [time and resources][1] to run. [1]: https://academic.oup.com/bioinformatics/article/30/7/923/232889#2676646 ...
written 10 days ago by arup1.4k
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Comment: C: see reads in .bam file, no counts after HTseq
... Are you using the same transcript file for alignment and HTseq? Also, I would recommend you to use [FeatureCounts][1] for transcript quantification. [1]: http://bioinf.wehi.edu.au/featureCounts/ ...
written 11 days ago by arup1.4k
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Comment: C: fastq dump usage of microRNA-seq data
... There is no problem if you use `--split-3 ` if the SRA entry doesn't contain paired-end reads the parameter will be ignored. I will recommend to first cache the SRA files using `prefetch` and then run `fastq-dump`. ...
written 17 days ago by arup1.4k
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Comment: C: extract polyformisms non synonymous using SnpSift
... Can you share a snippet of the vcf file including the header? ...
written 5 weeks ago by arup1.4k
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Comment: C: Annovar databases - where to get when annovar site is down?
... It's working fine now. ...
written 7 weeks ago by arup1.4k
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Comment: C: Strange MT% in 10X scRNA-seq data analysis
... Maybe there are two metabolically distinct subpopulations is present in the dataset. Also, the UMAP shows two distinct population of cells. I think there will not be any major issue if you consider the cells having <2% MT content, maybe these cells are differentiated and became metabolically less ...
written 7 weeks ago by arup1.4k
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Answer: A: Strange MT% in 10X scRNA-seq data analysis
... Can you plot the MT percent graph with `y.max =20` ? There can be several reasons for high mitochondrial content like 1) An issue during the library preparation. 2) A higher number of dead and dying cells. 3) MT content will vary among different cell types. According to most of the sources up t ...
written 7 weeks ago by arup1.4k

Latest awards to arup

Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: scatter plot in ggplot2 two colour for two different condition
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: scatter plot in ggplot2 two colour for two different condition
Guru 11 weeks ago, received more than 100 upvotes.
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: scatter plot in ggplot2 two colour for two different condition
Scholar 4 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Scholar 5 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Scholar 5 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Scholar 6 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: How to use Biopython for fetching metadata of NCBI/GenBank/RefSeq assembly ident
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Scholar 8 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
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Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Scholar 12 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
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