User: glady

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glady230
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Posts by glady

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Comment: C: Performing differential expression study on isoforms
... Yes, the counts are in integers. But if you use these counts as inputs to DESeq2, it gives you false results. Because the DESeq2 works very well for the gene counts and not for isoform counts, since the isoform are usually overlaps in the genes. ...
written 13 hours ago by glady230
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Comment: C: Performing differential expression study on isoforms
... RSEM gives you two files as output - "filename.genes.results" & "filename.isoforms.results. the second file contains the expected_counts on isoforms as well as the TPM counts. ...
written 16 hours ago by glady230
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Performing differential expression study on isoforms
... Hello, I have a RNAseq data(human) of 9 samples with 3 replicates each. the mapping to the reference was performed by STAR and quantification was done by RSEM. The differential expression study on genes was performed by DESeq2(taking the raw counts), but it failed for isoforms. 1) I ...
rna-seq written 16 hours ago by glady230 • updated 2 hours ago by Charles Warden5.2k
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Comment: C: Selecting the consensus/overlapped genes from the DE study
... Most of the genes are in the twilight zone. The intersection between the three is somewhere around 58%. While the intersection between limma & DESeq2 is 65%. ...
written 2 days ago by glady230
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Comment: C: Selecting the consensus/overlapped genes from the DE study
... Yes, you are right. I wanted to keep the results as stringent as I can for the downstream analysis. ...
written 2 days ago by glady230
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Comment: C: Selecting the consensus/overlapped genes from the DE study
... Thank you for your reply. DESeq2 & limma are good tools, you produce lower rates of false positives from these two tools as compared to the others. And this is according to the literature, **not from my results**. However, in my data as well I have observed the same. ...
written 2 days ago by glady230
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Comment: C: Selecting the consensus/overlapped genes from the DE study
... Is it okay to go ahead with the overlaps? Because even though I'm getting a good intersection(65%) between limma & DESeq2, the way read counts are normalized in limma & DESeq2 are different. I hope this doesn't create a problem for the reviewers. ...
written 2 days ago by glady230
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Selecting the consensus/overlapped genes from the DE study
... Hello everyone, I have 9 RNAseq samples(human), each with 3 replicates. I have performed the read mapping with STAR and quantification with RSEM. The differential expression(DE) study was performed by EBSeq, DESeq2 and limma. To keep our downstream analysis as stringe ...
rna-seq written 2 days ago by glady230 • updated 2 days ago by h.mon19k
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Tools for miRNA detection and analysis
... Hello everyone, I am new to the miRNA analysis work, I have some sample reads (human) which I need to map to the reference genome and then detect the number of miRNA present in it. I have done some literature survey on the algorithms which are used for the miRNA analys ...
rna-seq mirna written 6 months ago by glady230
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Functional genes from meta-genomes
... hello guyzz, I have some meta genomic data with me, my doubt is how can we detect functional targeted genes from a meta-genomic data sets ? ...
gene written 13 months ago by glady230

Latest awards to glady

Popular Question 6 months ago, created a question with more than 1,000 views. For MAUVE - genome alignment
Popular Question 6 months ago, created a question with more than 1,000 views. For Genome assembly tools
Popular Question 6 months ago, created a question with more than 1,000 views. For Using COG database
Popular Question 6 months ago, created a question with more than 1,000 views. For Extraction of 16S rRNA gene
Student 6 months ago, asked a question with at least 3 up-votes. For Russian gut microbiome
Student 6 months ago, asked a question with at least 3 up-votes. For Human gut metagenome data
Popular Question 12 months ago, created a question with more than 1,000 views. For Using COG database
Popular Question 17 months ago, created a question with more than 1,000 views. For Using COG database

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