User: devikaparvathy

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Posts by devikaparvathy

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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 4 weeks ago by devikaparvathy10
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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 4 weeks ago by devikaparvathy10
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Answer: 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 4 weeks ago by devikaparvathy10
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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 5 weeks ago by devikaparvathy10
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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 5 weeks ago by devikaparvathy10
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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 5 weeks ago by devikaparvathy10
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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 13 months ago by devikaparvathy10 • updated 12 months ago by Albert100

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Popular Question 13 months ago, created a question with more than 1,000 views. For Gene count table from STRINGTIE/BALLGOWN for WGCNA

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