User: Ankit

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Ankit110
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Posts by Ankit

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Comment: C: Normalization of allele specific counts in RNA-seq
... Hi, Thank you for the suggestion. So I posted here https://support.bioconductor.org/p/124191/ ...
written 22 days ago by Ankit110
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Comment: A: Normalization of allele specific counts in RNA-seq
... Hi, I would appreciate any suggestion. Thanks ...
written 22 days ago by Ankit110
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Comment: C: Normalization of allele specific counts in RNA-seq
... Thank you for sharing this link. The manual is well explained. What I understood is that author did not use size factor for normalization rather set the size factor to unity and calculated alternate vs reference allele ratios. There are few things, which I didn't get: **1.** In case you set the s ...
written 23 days ago by Ankit110
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Answer: A: Normalization of allele specific counts in RNA-seq
... Hi, I came across this tool called ISoLDE (https://www.bioconductor.org/packages/release/bioc/html/ISoLDE.html) for allele specific analysis. In the example data sets they have given both raw counts and normalized counts matrix. I wanted to know if there is similarity between factor used to normali ...
written 26 days ago by Ankit110
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Comment: C: Normalization of allele specific counts in RNA-seq
... Thanks for the suggestions. There are three things which I could think of now: 1. Set the size factor manually before running Deseq(). Which size factor to set? the one obtained from matrix before splitting? How to calculate that? If I set size factor will Deseq2 not calculate its own size factor ...
written 27 days ago by Ankit110
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Comment: C: Normalization of allele specific counts in RNA-seq
... Do you know if Deseq2 can take normalized counts by any chance? For example CPM normalized counts? ...
written 4 weeks ago by Ankit110
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Comment: C: Normalization of allele specific counts in RNA-seq
... So I am thinking to normalize by coverage (total reads mapped) of original total mapped reads. I will normalize both the alleles counts by the total reads mapped (before separating/assigning the reads = allele1+allele2+non-SNP reads). By dividing with total mapped reads, the bias of either allele du ...
written 4 weeks ago by Ankit110
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Comment: A: Normalization of allele specific counts in RNA-seq
... Hi, If anyone has a suggestion please let me know. I would appreciate any help. Thanks ...
written 4 weeks ago by Ankit110
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Comment: C: Normalization of allele specific counts in RNA-seq
... Hi, Thanks for the reply. So once after separating the allele-specific counts, I normalized these counts either by CPM or Deseq2 function. For now, let's focus on Deseq2, a single Deseq2 function [DESeq()] can both normalize and call differential expression. So, in this case, I have just given l ...
written 4 weeks ago by Ankit110
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Normalization of allele specific counts in RNA-seq
... Hi everyone, I am performing an allele-specific RNA-seq analysis. Basically, I used SNP positions between two alleles of a mouse hybrid strain to separate reads specific to each allele. Now I normalized the data, as usual, using Deseq2 function and performed differential expression analysis. Howe ...
normalization next-gen rna-seq snp allele-specific written 5 weeks ago by Ankit110

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Popular Question 5 months ago, created a question with more than 1,000 views. For Normalisation of RNAseq data and NOIseq

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