User: glady

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glady240
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Posts by glady

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Comment: C: Blast - Formatting Output
... How to give a mismatch parameter in blastn. I was to perform alignment allowing 1 mismatch. I'm going through a lot of parameters but can't find this one. ...
written 7 days ago by glady240
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Comparing novel miRNAs from miRDeep2
... Hello, How can I compare the novel miRNAs detected by miRDeep2 across different samples (based on their read counts)? For example, I have 3 samples(sample_1, sample_2,sample_3) from Condition-A. How can I check the read counts of say "novel_miR_1" from sample_1 with other 2 samples. I can't do this ...
rna-seq written 18 days ago by glady240
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"scale" parameter in MiRanda
... Hello all, I am using MiRanda for performing miR-target predictions on some 3'UTR sequences(hsa). I don't completely understand the "scale" parameter. I guess this parameter inclines to conservation in MiRanda. By default it is 4.0. But how to set this parameter? I mean, how can I g ...
rna-seq written 9 weeks ago by glady240
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score parameter in multimiR
... Hello everyone, Can anyone please guide me about the scoring parameter in multimiR. When you observe the table :View(example5@data). In this table you find a column 'score'. How are these scores calculated for every miR-target interactions? And how can we select inte ...
rna-seq written 9 weeks ago by glady240
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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 11 weeks 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 weeks 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 weeks 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 weeks 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 12 weeks 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 12 weeks ago by glady240

Latest awards to glady

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