User: glady

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glady260
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Posts by glady

<prev • 124 results • page 1 of 13 • next >
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protein - lncRNA interactions
... Hello everyone, I have an RNAseq data of a human cell line, with three experimental conditions(having 3 replicates each). The depth of all the samples is >80M. The same samples were also sequenced for small RNA(miRNAs), with help of some miRNA target prediction algorithms and databases I was abl ...
rna-seq written 7 weeks ago by glady260
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Assemblers and tools for MetaGenome and Metatranscriptomcs analysis
... Hello, I new to this field of Meta-omics. I do wanna know some recently updated tools/assemblers used for MetaGenome and MetaTransrciptomics analysis and annotation. Thanks for your help. ...
assembly next-gen alignment written 3 months ago by glady260
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Comment: C: miRNA target prediction
... Thank you very much for the suggestion, sir. Unfortunately, the link for the paper is broken. Can you please share it again? ...
written 7 months ago by glady260
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miRNA target prediction
... Hello all, I'm working on Human miRNA's, and I'm trying to predict miRNA targets in coding and non-coding genes. The algorithms(MiRanda, RNAhybrid, PITA) produce a lot of false positives and also there results differ significantly. So, now I use some online databases(TargetSCAN, starBase, miRtarbas ...
rna-seq written 7 months ago by glady260 • updated 7 months ago by Asaf8.4k
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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 11 months 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 11 months 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 11 months 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 11 months ago by glady260 • updated 11 months ago by kristoffer.vittingseerup3.4k
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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 15 months ago by glady260 • updated 15 months ago by i.sudbery9.2k
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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 18 months ago by glady260

Latest awards to glady

Popular Question 12 weeks ago, created a question with more than 1,000 views. For Circos - genome alignment
Popular Question 4 months ago, created a question with more than 1,000 views. For Retriving compounds name from KEGG IDs
Popular Question 4 months ago, created a question with more than 1,000 views. For Circos - genome alignment
Popular Question 7 months ago, created a question with more than 1,000 views. For Using COG database
Popular Question 7 months ago, created a question with more than 1,000 views. For Extraction of 16S rRNA gene
Popular Question 10 months ago, created a question with more than 1,000 views. For Protein Structure tools
Popular Question 10 months ago, created a question with more than 1,000 views. For Using COG database
Great Question 11 months ago, created a question with more than 5,000 views. For Using COG database
Popular Question 12 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 Genome assembly tools
Popular Question 15 months ago, created a question with more than 1,000 views. For Using COG database
Popular Question 19 months ago, created a question with more than 1,000 views. For Ray Meta assembler
Popular Question 20 months ago, created a question with more than 1,000 views. For Ray Meta assembler
Popular Question 22 months ago, created a question with more than 1,000 views. For Ray Meta assembler
Popular Question 23 months ago, created a question with more than 1,000 views. For Ray Meta assembler
Centurion 23 months ago, created 100 posts.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For MAUVE - genome alignment
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Genome assembly tools
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Using COG database
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Extraction of 16S rRNA gene
Student 2.5 years ago, asked a question with at least 3 up-votes. For Russian gut microbiome
Student 2.5 years ago, asked a question with at least 3 up-votes. For Human gut metagenome data
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Using COG database
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Using COG database

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