User: chudar.chudar

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Posts by chudar.chudar

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Answer: A: gene Isoforms quantification using RNA-seq data
... [RSEM][1] [1]: https://github.com/deweylab/RSEM ...
written 19 days ago by chudar.chudar0
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Comment: C: gene Isoforms quantification using RNA-seq data
... RSEM is best option you can go for ...
written 19 days ago by chudar.chudar0
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Comment: C: Removing Batch effect on the raw counts or normalised counts
... Thanks for your reply. But is there any other tool apart from DESeq2 which can remove the batch effect from raw or normalised counts ? Kindly guide me ...
written 19 days ago by chudar.chudar0
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Comment: C: Removing Batch effect on the raw counts or normalised counts
... Hi Michael, Thanks for your reply. I did include ~batch into my design to regress the batch effect. But I am wondering whether is it possible to have batch effect completely removed from raw counts or normalised counts. This is because I want to use batch effect removed raw or batch effect normalis ...
written 19 days ago by chudar.chudar0
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Removing Batch effect on the raw counts or normalised counts
... Dear All, I am a newbie to RNAseq data analysis. Recently I have RNA seq data which include 4 samples and each of the sample include triplicates. I used DESeq2 pipeline for analysing the data and in the PCA plot i could see that all rep1s from all 4 samples are clustered together and rep2 from all ...
rnaseq deseq2 batch effect written 19 days ago by chudar.chudar0 • updated 19 days ago by Michael Love25k
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Expected counts from RSEM in DESeq2
... Hi All, I am new to DESeq2 analysis and I follow the trinity pipeline for DESeq2 analysis. In that pipeline, RSEM is used to quantify the transcript abundance which generates the expected counts. These expected counts will be rounded off and later fed into DESeq2 pipeline for further analysis. I w ...
deseq2 rsem expected_counts raw_counts written 2.7 years ago by chudar.chudar0 • updated 2.7 years ago by Michael Love25k
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DESeq2 analysis for RNAseq data at different time points and different conditions
... Hi all, I am new to DESeq2 analysis. I have RNASeq raw count data from three different time points namely 0h, 10h, 2d. Every time point has triplicates for Control samples, Treatment-A, TreatmentB, TreatmentC. All I want to find is the differential expressed genes between Treated against Control sa ...
rnaseq timecourse deseq2 written 2.8 years ago by chudar.chudar0 • updated 2.8 years ago by Michael Love25k

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Popular Question 2.7 years ago, created a question with more than 1,000 views. For Expected counts from RSEM in DESeq2

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