User: rbenel

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rbenel0
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Posts by rbenel

<prev • 55 results • page 1 of 6 • next >
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Answer: A: Visualization for DE transcripts
... So in theory is isn't an issue to visualize the transcripts, if one follows a few steps. 1) Following using the `--writeMapping` flag when running `salmon` the pseudosam file needs to be sorted using `samtools` `samtools sort -o /path/to/output.bam /path/to/input.sam` 2) After sorting, the sorte ...
written 3 months ago by rbenel0
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Visualization for DE transcripts
... I am trying to find a way to visualize the different transcripts that I found to be DE using this workflow (https://bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html). I tried to re-run `salmon` and use the `--writeMapping` flag to receive a .sam file and then ...
rnaseqdtu written 3 months ago by rbenel0
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Comment: C: Importing Salmon counts with tximport with host and virus genomes
... Hi @michael Love, I know that `tximport` does gene summarization for every transcript, it is just that there are no transcripts in the virus (or at least not in the FASTA file I used)... but I understand what you mean, manually add the viral genes to the `tx2gene` object with the same name working ...
written 4 months ago by rbenel0
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Importing Salmon counts with tximport with host and virus genomes
... Hi, I have used `Salmon ` on some new RNAseq data that includes a host and virus (human and virus). When indexing the transcriptome, I concatenated the virus genome (as they don't have transcriptomes) to the .fatsa file of the host. I did the same with the .gtf file used for building the `txdb` obj ...
salmon tximport written 4 months ago by rbenel0 • updated 4 months ago by Michael Love25k
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Comment: C: stageR following DEXSeq two-stage analysis
... OK. Thank you for the detailed answer. ...
written 8 months ago by rbenel0
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Comment: C: stageR following DEXSeq two-stage analysis
... Yes, my question was how there can be evidence for a single transcript when in order for DTU to occur by definition there needs to be another transcript involved. I understand that there is a distinction between the underlying proportions v. statistical testing. So, what would you suggest one do w ...
written 8 months ago by rbenel0
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Comment: C: stageR following DEXSeq two-stage analysis
... Also, as a side note, what would be considered the minimum read depth for DTU detection? ...
written 8 months ago by rbenel0
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Comment: C: stageR following DEXSeq two-stage analysis
... I can look for a clearer case, but if the expression looks roughly similar, than I should not have gotten even a single significant transcript..? The error bars are SD. I "filtered" just to make my own script clear, but from the workflow, "The final table with adjusted p-values summarizes the inf ...
written 8 months ago by rbenel0
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stageR following DEXSeq two-stage analysis
... After running the `dex.padj <- getAdjustedPValues(stageRObj, order=FALSE, onlySignificantGenes=TRUE)`, and filtering for only the transcripts in the final table that are less than 0.05 I received a list of genes with only 1 transcript that was significant. I was curious to see what the expressi ...
rnaseqdtu written 8 months ago by rbenel0
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Comment: C: Differential transcript expression (DTE) analysis
... Yes, a total switch would be the most biologically interesting in this case... If something comes of the analysis I can post the code here in case it interests anyone else. Thanks Michael for all of the help :) ...
written 9 months ago by rbenel0

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