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User: Shalu Jhanwar

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Shalu Jhanwar • 470
Reputation:
470
Status:
Trusted
Location:
Switzerland
Last seen:
3 weeks, 6 days ago
Joined:
4 months, 4 weeks ago
Email:
s**************@gmail.com

Posts by Shalu Jhanwar

<prev • 58 results • page 1 of 6 • next >
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Comment: C: How I can study cross-talk from two different tissue using gene expression profi
... To map protein information of the gene, you may want to have a look at [UniProt][1]. For the DEGs in different tissues, the functional information at the protein level can be obtained from this resource. [1]: https://www.uniprot.org/help/uploadlists ...
written 4 weeks ago by Shalu Jhanwar • 470
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Answer: A: Retrieve Protein Sequences from Uniprot
... Have a look at the previous post [here][1] showing retrieval of the sequences from `UniProt` protein Ids. [1]: https://www.biostars.org/p/354555/ ...
written 5 weeks ago by Shalu Jhanwar • 470
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Answer: A: checking overlap between two genomic coordinates
... Have a look at [BedSect][1] and [Galaxy][2] online platforms. [1]: http://imgsb.org/bedsect/ [2]: https://usegalaxy.org/ ...
written 9 weeks ago by Shalu Jhanwar • 470
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Answer: A: How to Make Dot Plots of GO Terms?
... Have a look at dot plot with [ggplot][1] [1]: https://ggplot2.tidyverse.org/reference/geom_dotplot.html ...
written 9 weeks ago by Shalu Jhanwar • 470
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Answer: A: Phred qual error after fastq trimming
... I'd suggest first check quality encoding as suggested in this [post][1]. Then instruct Cutadapt to use correct quality scores. [1]: https://www.biostars.org/p/63225/ ...
written 9 weeks ago by Shalu Jhanwar • 470
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Answer: A: Extracting rows on basis of specific column values in R
... Suppose the entire protein Code Sequence is read in one column (codon) of the data frame. You can use the below code in R script to extract rows ends with "-2": grepl("-2$",df$codon) ...
written 9 weeks ago by Shalu Jhanwar • 470
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Answer: A: Using rsem-calculate-expression and STAR: invalid number of arguments?
... Without exact command generating the error, it's hard to pinpoint the bug. However, I'd suggest writing the whole command in one line, without the `\` character and run it. `\` causes issues sometimes. ...
written 9 weeks ago by Shalu Jhanwar • 470
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Answer: A: Gene Ontology Database
... Have a look at the gene ontology [site][1] that allows downloading of `GO database` in several formats. [1]: http://www-legacy.geneontology.org/GO.downloads.database.shtml ...
written 9 weeks ago by Shalu Jhanwar • 470
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Answer: A: multi species_gene name to description
... Have a look at `UniProt`. It contains multiple functional information (amino acid sequence, name or description, GO etc). [Here][1] is an example of it's functionality with the toy data you provided. You can add more columns by editing "columns" tab. [1]: https://www.uniprot.org/uniprot/?query=y ...
written 9 weeks ago by Shalu Jhanwar • 470
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Answer: A: New to NGS
... Have a look at RNA-seq analysis using [Galaxy][1]. It's quite useful for beginners to give a flavor of analysis steps. An advantage is that you may try out other types of omics data analysis as well using this platform. [1]: https://galaxyproject.org/tutorials/rb_rnaseq/ ...
written 10 weeks ago by Shalu Jhanwar • 470

Latest awards to Shalu Jhanwar

Scholar 8 weeks ago, created an answer that has been accepted. For A: Failed to merge BAM files
Scholar 9 weeks ago, created an answer that has been accepted. For A: Failed to merge BAM files
Rising Star 9 weeks ago, created 50 posts within first three months of joining.
Scholar 10 weeks ago, created an answer that has been accepted. For A: Failed to merge BAM files
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Whole Genome Sequencing Data Annotation
Scholar 3 months ago, created an answer that has been accepted. For A: Failed to merge BAM files
Scholar 3 months ago, created an answer that has been accepted. For A: Failed to merge BAM files
Scholar 3 months ago, created an answer that has been accepted. For A: Failed to merge BAM files
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Whole Genome Sequencing Data Annotation
Scholar 3 months ago, created an answer that has been accepted. For A: Failed to merge BAM files
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