User: devikaparvathy

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New User
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India
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4 weeks ago
Joined:
4 years, 1 month ago
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d*************@gmail.com

Posts by devikaparvathy

<prev • 10 results • page 1 of 1 • next >
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Meta-Analysis p-value combining and adjusting
... I am conducting a meta-analysis from different RNA-Seq/Microarray datasets of the same hypothesis (Control vs a specific test condition, for example). While combining p-values from the multiple DEG experiments , should the raw p-values be used for combining and then adjusted or can the adjusted p-va ...
metaanalysis p-value adjustment microarray rna-seq written 28 days ago by devikaparvathy20 • updated 27 days ago by mark.ziemann1.1k
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Comment: A: Paired end reads merged to single end for mapping - should i allow multi-overlap
... No, multimapping and multioverlapping are different. I checked this by running alternate featurecount analysis on the same dataset by changing each of the option to true and false and analysing the results. Multioverlapping when kept to false, produces many ambiguous, and the counts for lot of genes ...
written 10 months ago by devikaparvathy20
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Paired end reads merged to single end for mapping - should i allow multi-overlap similar to paired end reads?
... I am using featurecounts after mapping of my reads. I have a paired-end sequencing data but Only a low percentage of reads were mapped when the paired-end reads were mapped separately and hence they were merged to a single-end read and mapped. I know that when we use paired-end reads in featurecou ...
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Comment: C: Cross-species RNA-seq analysis in bacteria
... My aim is to do an integrative analysis of certain public RNA-seq data available for a particular bacterial species. But each experiment are done in different strains/subspecies. What I plan to do is to align the reads to their respective reference genomes, and for further analysis, create an annot ...
written 12 months ago by devikaparvathy20
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Answer: A: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
... Can I use this liftover to map co-ordinates between bacterial subspecies? My aim is to do an integrative analysis of certain public RNA-seq data available for a particular bacterial species *S. aureus*. But each experiment are done in different strains/subspecies. What I plan to do is to align the ...
written 12 months ago by devikaparvathy20
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Comment: A: Cross-species RNA-seq analysis in bacteria
... Hi, thank you for your reply. But I doubt if I want to create a new consensus reference genome and carry out the analysis - in that case will all the corresponding genes be mapped correctly? ...
written 12 months ago by devikaparvathy20
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Comment: C: Gene count table from STRINGTIE/BALLGOWN for WGCNA
... Hello devikaparvathy! We believe that this post does not fit the main topic of this site. The issue was resolved. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply ...
written 12 months ago by devikaparvathy20
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Comment: C: Gene count table from STRINGTIE/BALLGOWN for WGCNA
... Sorry i had somehow missed your comment, I was working on a prokaryotic dataset and hence used BowTie. I used cufflinks suit to obtaine the normalized gene count. ...
written 12 months ago by devikaparvathy20
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Cross-species RNA-seq analysis in bacteria
... Hi, I am working on microbial genomics, and there are a couple of datasets in SRA/ENA that I can use for my work. I want to combine these datasets in a single study but the problem is these datasets are all done on different subspecies of *S. aureus.* I tried creating a common reference genome a ...
bacteria rna-seq multiple datasets written 12 months ago by devikaparvathy20
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(Closed) Gene count table from STRINGTIE/BALLGOWN for WGCNA
... I am using Bowtie+Stringtie+Ballgown for differential expression analysis of certain microbial RNA-seq data. I also want to create a whole genome regulatory networks using WGCNA package. Is it possible to obtain NORMALIZED COUNT table from Stringtie/Ballgown to use in WGCNA? (I have previously used ...
wgcna stringtie ballgown rna-seq written 2.0 years ago by devikaparvathy20 • updated 23 months ago by Albert140

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Popular Question 2.0 years ago, created a question with more than 1,000 views. For Gene count table from STRINGTIE/BALLGOWN for WGCNA

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