User: Shalu Jhanwar
Shalu Jhanwar • 480
- Reputation:
- 480
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- Location:
- Switzerland
- Last seen:
- 2 weeks, 6 days ago
- Joined:
- 8 months ago
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Posts by Shalu Jhanwar
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... 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 months ago by
Shalu Jhanwar • 480
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... 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 4 months ago by
Shalu Jhanwar • 480
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... Have a look at [BedSect][1] and [Galaxy][2] online platforms.
[1]: http://imgsb.org/bedsect/
[2]: https://usegalaxy.org/ ...
written 5 months ago by
Shalu Jhanwar • 480
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... Have a look at dot plot with [ggplot][1]
[1]: https://ggplot2.tidyverse.org/reference/geom_dotplot.html ...
written 5 months ago by
Shalu Jhanwar • 480
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... 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 5 months ago by
Shalu Jhanwar • 480
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... 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 5 months ago by
Shalu Jhanwar • 480
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... 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 5 months ago by
Shalu Jhanwar • 480
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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 5 months ago by
Shalu Jhanwar • 480
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... 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 5 months ago by
Shalu Jhanwar • 480
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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 5 months ago by
Shalu Jhanwar • 480
Latest awards to Shalu Jhanwar
Rising Star
5 months ago,
created 50 posts within first three months of joining.
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: Whole Genome Sequencing Data Annotation
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: Whole Genome Sequencing Data Annotation
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