User: arup
arup • 1.4k
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PhD student @ Institute of Life Science, Bhubaneswar
Posts by arup
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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
arup • 1.4k
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84
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... Check the `row.names` column with `uniq -d` to see if any duplicate gene/transcript id present. ...
written 10 days ago by
arup • 1.4k
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... Can you share more details like platform used for the experiment and how you got the fastq files? ...
written 10 days ago by
arup • 1.4k
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130
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... 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
arup • 1.4k
2
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1
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130
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... 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
arup • 1.4k
2
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129
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... 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
arup • 1.4k
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1
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132
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... Can you share a snippet of the vcf file including the header? ...
written 5 weeks ago by
arup • 1.4k
1
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1
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144
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... It's working fine now. ...
written 7 weeks ago by
arup • 1.4k
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... 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
arup • 1.4k
4
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1
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232
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... 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
arup • 1.4k
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