User: sangram_keshari
sangram_keshari • 120
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Bioinformatics Student, Working in the field of Computational Genomics.
Posts by sangram_keshari
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... Here is a PCA plot: https://imgur.com/a/sv6zEw8
Towards extreme left the PE datasets and towards extreme right SE. ...
written 4 weeks ago by
sangram_keshari • 120
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... After normalization also, The scaling in both the datasets is different, which is not comparable.
Note: I want to compare relative expression. ...
written 4 weeks ago by
sangram_keshari • 120
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... I want to compare the gene expression of similar tissue-type coming from one SE and another PE dataset (each having 3 biological replicates in both). And also both are from different labs with different protocols.
So I tried to normalize both the datasets with `normTransform` in DESeq2 package fro ...
written 4 weeks ago by
sangram_keshari • 120
• updated
4 weeks ago by
johnsonnathant • 80
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... Yes, but also it has few functions for a seamless integration with few outputs from other packages:
According to that Bioconductor vignettes link shared by @WouterDeCoster:
> the tximport pipeline offers the following benefits: (i) this approach corrects for potential changes in gene length acr ...
written 3 months ago by
sangram_keshari • 120
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... Yes, this pipeline is a better choice. ...
written 3 months ago by
sangram_keshari • 120
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... The vertical line is a separation of the single sequence with different alignment score and the horizontal line between green and red is a separation in the same sequence where alignment score is different for different regions.
Hope that helped. ...
written 3 months ago by
sangram_keshari • 120
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... Basically, NumReads will have quantified reads mapped to each transcript. Yes, you can use them.
Once quantified, You can use other tools like - `edgeR` and `DESeq2` for DEG. ...
written 3 months ago by
sangram_keshari • 120
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... May I know, You want to compare conditions or have a control to compare with?
In terms of Matrix design. Yes, if you doing with multiple conditions then the second command will come handy. ...
written 3 months ago by
sangram_keshari • 120
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... I suppose, If you do have RAW expression values then also you can create co-expression matrix! ...
written 3 months ago by
sangram_keshari • 120
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... Yes, I completely agree. Even I encourage people to do with StrigTie (Because of its improvements in efficiency)
As a matter of doubt in the question dealing with Cufflinks, I tried to explain where it might be going wrong. ...
written 3 months ago by
sangram_keshari • 120
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