User: glady

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glady260
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Posts by glady

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Comment: C: Queries regarding RNASeq sequencing
... Thank you for your useful suggestions. Can you share some links with me about such literatures, it would be really helpful. ...
written 5 weeks ago by glady260
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Comment: C: Queries regarding RNASeq sequencing
... I'm sorry but can you provide me some more details on this point. How can I cluster the samples on their expression? Are there any kinds of literature where they have performed similar work? ...
written 5 weeks ago by glady260
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Comment: C: Queries regarding RNASeq sequencing
... How can I co-relate my expression dataset with TCGA, to identify the enriched pathways or genes? Are there any R packages which I can used to do so? Or any other tutorials? ...
written 5 weeks ago by glady260
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Queries regarding RNASeq sequencing
... Hello all, I have some very simple questions regarding Human transcriptome sequencing: 1) Which library size would be better for sequencing: 1x150 or 2x75? 2) What can I consider as a good depth for performing the transcriptomic analysis: 20M, 30M or >30M? 3) Can we perform the transcriptomic ...
rna-seq written 5 weeks ago by glady260 • updated 5 weeks ago by kristoffer.vittingseerup2.8k
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Pathway Enrichment on lncRNAs
... Hello everyone, I'm working on transcriptomic data of human samples, for which I have detected more than 100 expressed lincRNAs. I want to perform a pathway enrichment study on these lncRNAs, How am I supposed to this? Because, I have the Ensembl Gene_IDs and Gene.Symbols for these lincRNAs, but ...
rna-seq written 5 months ago by glady260 • updated 5 months ago by i.sudbery6.3k
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Comment: C: Using MiRanda for miRNA - PCG interactions
... Thank you very much for your replies. With MiRanda, it's very difficult to find "biologically true" targets which follow the conservation parameter. With TargetSCAN I did got some decent results, out of the total 600 miRs & 10300 PCGs, TargetSCAN in total predicted 9302 interactions (215 miRNAs ...
written 8 months ago by glady260
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Comment: C: Using MiRanda for miRNA - PCG interactions
... I tried to filter them for a higher alignment score(>140) & a lower binding energy(<=-20), but there is hardly any change. The output file still has a target gene for every possible miRNA(all the 600). I think that conservation parameter is more important in predicting the "biologically t ...
written 8 months ago by glady260
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Comment: C: Using MiRanda for miRNA - PCG interactions
... If the commands are right then why there are so many false positives? Because, biologically it's very difficult to conclude that every miRNA will have atleast one target gene & vice versa. The results I'm getting are very complicated and confusing. ...
written 8 months ago by glady260
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Comment: C: Using MiRanda for miRNA - PCG interactions
... In my analysis, I observed 2 things; 1) **every miRNA targets at least one gene(all the 600 expressed miRs have at least one target gene)** 2) **almost every gene(10290 PCGs out of the total 10300 PCGs) is targeted by at least one miRNA.** I hope, I'm clear. Yes, you are right MiRanda has a high f ...
written 8 months ago by glady260
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Using MiRanda for miRNA - PCG interactions
... Hello everyone, I working on some human samples, I have their mRNA and the miRNA dataset in triplicates. Now, I'm interested in studying the miRNA - Protein Coding Gene (PCG) interactions using these dataset. Hence, I used MiRanda, but the results which I get are more ...
rna-seq written 8 months ago by glady260 • updated 8 months ago by i.sudbery6.3k

Latest awards to glady

Great Question 5 weeks ago, created a question with more than 5,000 views. For Using COG database
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Genome assembly tools
Popular Question 5 months ago, created a question with more than 1,000 views. For Genome assembly tools
Popular Question 5 months ago, created a question with more than 1,000 views. For Using COG database
Popular Question 10 months ago, created a question with more than 1,000 views. For Ray Meta assembler
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Popular Question 12 months ago, created a question with more than 1,000 views. For Ray Meta assembler
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Centurion 13 months ago, created 100 posts.
Popular Question 21 months ago, created a question with more than 1,000 views. For MAUVE - genome alignment
Popular Question 21 months ago, created a question with more than 1,000 views. For Genome assembly tools
Popular Question 21 months ago, created a question with more than 1,000 views. For Using COG database
Popular Question 21 months ago, created a question with more than 1,000 views. For Extraction of 16S rRNA gene
Student 21 months ago, asked a question with at least 3 up-votes. For Russian gut microbiome
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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Using COG database
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