User: sangram_keshari

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Bioinformatics Student, Working in the field of Computational Genomics.

Posts by sangram_keshari

<prev • 51 results • page 1 of 6 • next >
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Comment: C: Compare SE and PE gene expression data.
... 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_keshari120
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Comment: C: Compare SE and PE gene expression data.
... 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_keshari120
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Compare SE and PE gene expression data.
... 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 ...
deseq2 rna-seq written 4 weeks ago by sangram_keshari120 • updated 4 weeks ago by johnsonnathant80
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Comment: C: May I use numreads for doing DGE after quantifying by Salmon
... 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_keshari120
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Comment: C: May I use numreads for doing DGE after quantifying by Salmon
... Yes, this pipeline is a better choice. ...
written 3 months ago by sangram_keshari120
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Answer: A: Graphical output of Blast. What are grey and black lines?
... 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_keshari120
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Answer: A: May I use numreads for doing DGE after quantifying by Salmon
... 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_keshari120
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Comment: C: General Question to shRNA-Seq analysis
... 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_keshari120
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Comment: C: mutual rank values for distance matrix formation for co-expression analysis
... I suppose, If you do have RAW expression values then also you can create co-expression matrix! ...
written 3 months ago by sangram_keshari120
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Comment: C: Identifying novel isoforms from RNAseq data
... 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_keshari120

Latest awards to sangram_keshari

Scholar 8 months ago, created an answer that has been accepted. For A: cuffcompare: No novel genes found. Is this possible?
Supporter 12 months ago, voted at least 25 times.
Autobiographer 14 months ago, has more than 80 characters in the information field of the user's profile.

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