User: glady

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glady250
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Posts by glady

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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 8 days ago by glady250 • updated 8 days ago by i.sudbery4.8k
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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 12 weeks ago by glady250
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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 12 weeks ago by glady250
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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 12 weeks ago by glady250
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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 12 weeks ago by glady250
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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 12 weeks ago by glady250 • updated 12 weeks ago by i.sudbery4.8k
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Comment: C: Comparing novel miRNAs from miRDeep2
... Thank you very much for your reply. Yes, I agree with you the mirDeep2 output is quite obscure and elusive for novel miRNAs. Because the provisional id's contains a random number after the chromosome number, which is different in every sample. What I did was to remove the miRNAs having the same p ...
written 4 months ago by glady250
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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 5 months ago by glady250
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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 5 months ago by glady250 • updated 4 months ago by v82masae140
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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 7 months ago by glady250

Latest awards to glady

Popular Question 4 months ago, created a question with more than 1,000 views. For Ray Meta assembler
Popular Question 5 months ago, created a question with more than 1,000 views. For Ray Meta assembler
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Centurion 7 months ago, created 100 posts.
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Popular Question 15 months ago, created a question with more than 1,000 views. For Genome assembly tools
Popular Question 15 months ago, created a question with more than 1,000 views. For Using COG database
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Popular Question 21 months ago, created a question with more than 1,000 views. For Using COG database
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