User: antoinefelden

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Posts by antoinefelden

<prev • 14 results • page 1 of 2 • next >
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Answer: A: How to deal with single transcripts assigned to multiple genes?
... Okay, I solved that problem, which was not really one but in fact a feature of StringTie. See https://github.com/gpertea/stringtie/issues/170 In a nutshell, there is an alternative - simpler - StringTie pipeline that skip the assembly step. So what this does is simply to map the reads, without loo ...
written 2 days ago by antoinefelden20
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Is it okay to remove uncharacterised transcripts from downstream analysis in RNA-seq?
... I work with a reference genome that is only partially annotated, and I'm wondering if it's okay for me to discard uncharacterised genes from my dataset (once I've properly calculated TMM-normalisation factors from all transcripts, including the uncharacterised ones). I can deal with having lots of ...
wgcna rna-seq dge written 3 days ago by antoinefelden20
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How to deal with single transcripts assigned to multiple genes?
... After I ran StringTie after Hisat2 on a non-model RNA-seq data set (i.e. Argentine ant), I realised that some StringTie transcripts were assigned to multiple genes (see exemple below) which is causing many problems down the line. 24887 MSTRG.1473 LOC105670921 24920 MSTRG.1473 LOC1056707 ...
stringtie rna-seq hisat2 written 3 days ago by antoinefelden20 • updated 1 day ago by RamRS17k
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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 10 months ago by antoinefelden20
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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 10 months ago by antoinefelden20
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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 10 months ago by antoinefelden20
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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 18 months ago by antoinefelden20
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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 21 months ago by antoinefelden20
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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 22 months ago by antoinefelden20
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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 22 months ago by antoinefelden20

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Popular Question 9 months ago, created a question with more than 1,000 views. For Target fragment size versus final insert size

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