User: antoinefelden

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Posts by antoinefelden

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Is it valid to compare the expression of pre-defined candidate genes from RNA-se
... A bit of background: I work on a non-model organism - the Argentine ant - that does have a sequenced genome but limited annotation, and no actual functional characterisation. Which is why I try to look at the big picture as much as I can, because not much is known in the genes that turned out to be ...
written 7 months ago by antoinefelden10
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Answer: A: Is it valid to compare the expression of pre-defined candidate genes from RNA-se
... To be specific, I'm trying to investigate if immune genes show condition-specific expression profiles. I first produced heatmaps with a set of immune genes that do show consistent differences between conditions across replicates. Then, I did a simple `glm(scale(log2(TMMs))~condition)` that showed si ...
written 7 months ago by antoinefelden10
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Is it valid to compare the expression of pre-defined candidate genes from RNA-seq data?
... Hi, In addition to a classic differential expression analysis, I'd like to investigate the expression of pre-defined 'candidate genes' from my RNA-seq data. What I've done: from a TMM-normalised transcript quantification matrix (the same kind of matrix that is leveraged by differential expression ...
rna-seq written 7 months ago by antoinefelden10
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Comment: C: Target fragment size versus final insert size
... I ran BBMap (with BBwrap) to align my PE reads to a reference genome, which gave me a single sorted bam file as an output. Then I'm using reformat.sh as above to make Trinity work with it. However, a warning message got my attention: "Input is being processed as unpaired" while I originally had pair ...
written 15 months ago by antoinefelden10
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Comment: C: Target fragment size versus final insert size
... Hi Brian, Just letting you know that I ended up having to use another aligner than BBmap, as the BAM output doesn't have the right CIGAR alignment formatting to be taken as input by Trinity (rna-seq). Have a look at this thread for more details: https://groups.google.com/forum/#!topic/trinityrnaseq ...
written 19 months ago by antoinefelden10
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Comment: C: TopHat2: "IOError: [Errno 28] No space left on device" with large input
... I will use others but I wanted to compare outputs (namely with BBTools, I haven't looked at hisat2 or STAR). Since temporary files seem to be the issue here, is there any way to tell TopHat where to stick them somewhere else than the local work area? ...
written 19 months ago by antoinefelden10
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Comment: C: TopHat2: "IOError: [Errno 28] No space left on device" with large input
... I work on my university HPC, on Linux. I'm running TopHat to align 15*2 read files (~8 GB each), with the --read-realign-edit-dist option which is known to increase computing time and maybe memory requirements as well? All the raw files are copied into the working space before the TopHat run starts, ...
written 19 months ago by antoinefelden10
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TopHat2: "IOError: [Errno 28] No space left on device" with large input
... I'm trying to run TopHat2 on my RNA-seq sample, but while trial job with a small subset of my samples worked fine, I can't run it with my full dataset. The trial run took around 30 GB as input, and everything went smooth, but when I tried with the full dataset of ~250 GB, then I got the following e ...
tophat2 memory usage rna-seq written 19 months ago by antoinefelden10
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Comment: C: Target fragment size versus final insert size
... The BBmerge-auto command with your parameters gave an average insert size of 245 +/- 62. The BBmap with pairlen=1000 gave a value of 248 +/- 72. Similar values, and close to the BWA estimate. Sounds good to me! Thanks Brian, I will look into the rest of the package ;-) ...
written 19 months ago by antoinefelden10
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Comment: C: Target fragment size versus final insert size
... Hi Brian, Thanks, I haven't explore other functions yet but indeed BBmap is doing a good job to give insert size, fast and easy. I ran a alignment-free version to compare it with the genome-guided one. The former gave me an insert size of 219 +/- 40 while the genome-guided one gives a value of 269 ...
written 19 months ago by antoinefelden10

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Popular Question 7 months ago, created a question with more than 1,000 views. For Target fragment size versus final insert size

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