User: devikaparvathy

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New User
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India
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1 month, 3 weeks ago
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3 years, 4 months ago
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Posts by devikaparvathy

<prev • 9 results • page 1 of 1 • next >
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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 7 weeks ago by devikaparvathy10
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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 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 16 months ago by devikaparvathy10 • updated 14 months ago by Albert100

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Popular Question 16 months ago, created a question with more than 1,000 views. For Gene count table from STRINGTIE/BALLGOWN for WGCNA

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