## User: rbenel

rbenel0
Reputation:
0
Status:
New User
Last seen:
2 months, 2 weeks ago
Joined:
2 years, 2 months ago
Email:
r*************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

#### Posts by rbenel

<prev • 55 results • page 1 of 6 • next >
2
166
views
2
... 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
2
166
views
2
... 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 ...
written 3 months ago by rbenel0
1
118
views
1
... 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
1
118
views
1
... 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 ...
written 4 months ago by rbenel0 • updated 4 months ago by Michael Love25k
1
195
views
1
... OK. Thank you for the detailed answer. ...
written 8 months ago by rbenel0
1
195
views
1
... 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
1
195
views
1
... Also, as a side note, what would be considered the minimum read depth for DTU detection? ...
written 8 months ago by rbenel0
1
195
views
1
... 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
1
195
views
1
... 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 ...
written 8 months ago by rbenel0
1
331
views
1
... 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

#### Latest awards to rbenel

No awards yet. Soon to come :-)

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.