User: António Miguel de Jesus Domingues
- Reputation:
- 430
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- Location:
- Germany
- Website:
- http://adomingues.gith...
- Last seen:
- 4 days, 7 hours ago
- Joined:
- 7 years, 1 month ago
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Posts by António Miguel de Jesus Domingues
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... I am also having problems replicating it so it is likely that at some I made a mistake. I will add a note at the top of the post. Apologies for the time lost but I was certain that something was going on.
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written 4 months ago by
António Miguel de Jesus Domingues • 430
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... I actually tried to create a smaller example in the same way, and like you also failed. That is why I mention that this could be a localized issue. That said, I will try to replicate with a small subset of and get back to you.
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written 4 months ago by
António Miguel de Jesus Domingues • 430
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... See my answer here: https://www.biostars.org/p/351612/#352575
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written 4 months ago by
António Miguel de Jesus Domingues • 430
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... IGNORE this issue. It is likely that I did something wrong at some point since I am having problems reproducing the problem myself.
tldr: it seems that after `collapseReplicates` the levels of newly created factors are shifted affecting the results. **If** this observation is correct and not a d ...
written 4 months ago by
António Miguel de Jesus Domingues • 430
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... Hi konstatinos,
The majority of reads multimap to different piRNAs, I took the sum of reads assigned to each piRNA (both unmatched/matched reads to the genome).
Maybe I misunderstood, but does this mean that a read is counted more than once? Each read should be counted only once. If you want to u ...
written 4 months ago by
António Miguel de Jesus Domingues • 430
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... Sorry for the belated reply, but working on other things got in the way. Thank your for the clarification regarding the separate call for each range - I had no idea it worked that way. For now I am sticking with GenomicAlignments followed by GR. Memory might be an issue down the line, but having re ...
written 5 months ago by
António Miguel de Jesus Domingues • 430
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... Dear BioC team,
I am trying to leverage the power of Rsamtools to summarize reads in a number of ways. For instance, read length (seq) of reads mapping to certain genes. Here is simplified version of one my functions:
library("Rsamtools")
get_seq_lengths <- function(bamPath, coordinates = NULL){ ...
written 6 months ago by
António Miguel de Jesus Domingues • 430
• updated
6 months ago by
Martin Morgan ♦♦ 23k
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... I downloaded data for an RNA-seq experiment using the ExpressionAtlas package - very very straightforward by the way. Sadly the data contains only the raw counts from said experiment, whereas my expectation was that one would also get access to the pre-calculated RPKM/TPM since these are available ...
written 16 months ago by
António Miguel de Jesus Domingues • 430
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...
> library(biomaRt)
> packageVersion("biomaRt")
[1] ‘2.35.2’
## [1] 97 3
## [1] "Is drerio present? TRUE"
All systems are go :) Thank you for the fix.
...
written 16 months ago by
António Miguel de Jesus Domingues • 430
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... Good tip. In my case it was a little lazy because I am also using the script to run some C. elegans data analysis and this will work for both - RIPSeeker needs biomaRt/ensembl so I need an archive version before the move to Wormbase. Another hack.
...
written 16 months ago by
António Miguel de Jesus Domingues • 430
Latest awards to António Miguel de Jesus Domingues
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For problems generating a gene2GOlist in topGO
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For Gviz - show plus and minus strand from a bam
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