User: ponganta

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ponganta50
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Master student working on transcriptomics of a non-model species.

Posts by ponganta

<prev • 12 results • page 1 of 2 • next >
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Homolog-level DGE analyses - what to consider?
... Hello, I'm currently working on tissue-specific RNAseq data of a non-model polyploid, which is however closely related to a model species. My goal is to identify tissue-specific DEGs via pairwise comparisons. I approached this task by: 1. de novo assembly of transcripts 2. annotation 3. quanti ...
deseq2 rna-seq differential gene expression written 8 days ago by ponganta50
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Comment: C: Does read length of RNA seq affects the results ?
... Unfortunately, the OP also states that both libraries were constructed in different experiments, hence the likely batch effect I mentioned. Sorry for my imprecise wording! Maybe [comBat][1] will be of use here? But to @chaudharyc61: I doubt that you can succesfully conduct DGE-analyses in this situa ...
written 11 days ago by ponganta50
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Comment: C: Merging Transcriptomes from different assemblers
... Thanks for the offer, although in the end I simply conducted several naive assemblies (Trinity, rnaSPAdes & a custom hybrid pipeline for ONP + illumina). I then simply picked the highest quality one (based on technical & biological metrics). Although transcriptome merging is being held as po ...
written 12 days ago by ponganta50
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Comment: A: Unexpected gene polymorphism using Salmon-tximeta-DESeq2
... I think the problem is that you simply conducted transcript-level DGE-analysis. What kind of organism are you using? What reference did you use? How did you annotate your transcripts? Maybe you should use [tximport][1] to conduct gene-level DGE analyses as recommended in [this paper][2]. tximport ba ...
written 12 days ago by ponganta50
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Answer: A: Does read length of RNA seq affects the results ?
... What kind of analyses do you want to conduct? How do you quantify (mapping or quasi mapping?), what kind of reference do you utilise? Do you want to compare WT and mutant under certain conditions? To add to @ATpoint and @GenoMax, if you want to find DEGs between WT and mutant, you might see a prett ...
written 12 days ago by ponganta50
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Answer: A: BayesHammer in SPAdes
... Hello, I'd suggest simply using [rCorrector][1] instead of manually trying BayesHammer. The program is also part of the [Oyster River Protocol][2] and is [recommended][3] to be used prior to de novo transcriptome assembly. rCorrector can simply be installed in a conda environment. If you really wan ...
written 12 days ago by ponganta50
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Comment: C: Kmeans in R for clustering on significant gene list by sample
... Would you actually use those counts (as in transformed CPM), or would you rather conduct feature scaling using using the z-score prior to clustering (as in base::scale)? Thank you! ...
written 7 weeks ago by ponganta50
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Obtaining Gene Expression patterns via Kmeans - clustering sample means or linear models?
... Hi there, I'm a novice in analysing gene expression data and have some difficulties going forward. Especially because I have no profound knowledge of modelling. Following the identfication of differentially expressed genes (DEGs) using DESeq2, I want to classify DEGs according to their expression p ...
R modelling rna-seq expression patterns written 10 weeks ago by ponganta50
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Comment: C: How to make k-means clustering plot for relative expression?
... How exactly did you standardize your gene expession levels? ...
written 3 months ago by ponganta50
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Merging Transcriptomes from different assemblers
... Hello all, currently I'm working on the de novo assembly of a non-model plant. I've got tissue-specific illumina-, as well as whole-plant ONP-cDNA-reads. My current plans are as follows: 1. Conducting master-assemblies (short read & Hybrid) using the three best assemblers out there (Trinity, t ...
assembly rna-seq written 7 months ago by ponganta50

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