User: glady

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glady240
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Posts by glady

<prev • 105 results • page 1 of 11 • next >
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Comment: C: Which normalization method to use FPKM/TPM?
... I divided the read counts by total no. of reads in the sample, instead of "total number of mapped reads". I guess, this was the mistake ...
written 10 days ago by glady240
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Comment: C: RSEM output interpretation
... probably its a bug, I don't know the exact reason why, but its an error. I used RSEM a number of times, but there was never such a situation. ...
written 11 days ago by glady240
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Calculating RPM for miRNA
... Hello, While calculating RPM the read counts should be divided by : total number of **MAPPED READS** from a given library or by the total number of reads in the sample ? Thank you. ...
rna-seq written 11 days ago by glady240
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Comment: C: Which normalization method to use FPKM/TPM?
... Should the sum of the RPM column be precisely 1 M, for each miRNA sample? Because now when I calculate the sum of RPM, it is around 0.5 million ...
written 11 days ago by glady240
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Comment: C: RSEM output interpretation
... It Shouldn't be like this. Probably there is some problem with the parameters you are using. ...
written 14 days ago by glady240
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Comment: C: Which normalization method to use FPKM/TPM?
... For studying the differentially expressed transcripts/isoforms, can we use the raw counts. Because most of the algorithms give a strange output when isoform raw counts are used as inputs for differential expression study. Eg, DESeq2, limma. I was planning to use tximport on the isoform raw counts ...
written 15 days ago by glady240
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Comment: C: Which normalization method to use FPKM/TPM?
... Thank you for the comments. ...
written 15 days ago by glady240
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Comment: C: Which normalization method to use FPKM/TPM?
... Okay, thank you for the explanation. ...
written 15 days ago by glady240
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Comment: C: Which normalization method to use FPKM/TPM?
... I didn't understand the fourth condition. How different is the fourth condition (A vs B vs C) from the above three? What different results should we except from this? How would I interpret its results? Because we might already get the list of DE genes & isoforms from the first three condition. ...
written 15 days ago by glady240
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Comment: C: Which normalization method to use FPKM/TPM?
... For miRNA samples, is there a need to consider the gene length while calculating the normalized counts like rpkm? Since, the all the miRNA have almost the same length. ...
written 15 days ago by glady240

Latest awards to glady

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