User: Barry Digby
Barry Digby • 250
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- @BarryDigby
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Posts by Barry Digby
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... I think I may not have been very clear. I am referring specifically to the genes.txt output from `bustools count`. In the second link you provided me, the dataset has a `genes.tsv` file, that has both ENSG ID + symbols. In my own attempts using `bustools count`, my output has only ENSG ID. This make ...
written 1 day ago by
Barry Digby • 250
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... Thanks for the response Páll.
I'll integrate the `py` script into my nextflow script and hopefully get to the bottom of this over the weekend.
I've noticed the ensembl GTF file uses version Id's but the ensembl cDNA file does not. Annoying discrepancy. Anyway I'll get to work and post a solution ...
written 3 days ago by
Barry Digby • 250
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... No. Clustering is unsupervised... ...
written 4 days ago by
Barry Digby • 250
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... Hi, quick question,
For the bustools output, is the `.genes.txt` file supposed to contain matching gene symbols in the output? Reading this [galaxy tutorial](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/scrna-scanpy-pbmc3k/tutorial.html#data) suggests cellrang ...
written 4 days ago by
Barry Digby • 250
• updated
3 days ago by
pmelsted • 110
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... I just had a quick look at the salmon "getting started" page and they use ```Arabidopsis_thaliana.TAIR10.28.cdna.all.fa.gz``` as the reference for the tutorial. I think we mean the same thing when we say transcriptome/cDNA :)
I've tried comparing the two files as you suggested using h.sapiens but ...
written 5 days ago by
Barry Digby • 250
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... Thank you ATpoint and Emily.
I am still a bit confused as to why 'kallisto assets' would provide a tx2gene file based on an all encompassing GTF file, when the reads are aligned to the cDNA reference? Or am I missing something obvious. ...
written 5 days ago by
Barry Digby • 250
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... Time for a different approach: If I were you, I would start to generate some sample to sample plots to show that there is not much 'distance' between the samples, hence the poor results. You can't just say it didn't work, you have to show why. They would complement the PCA plot. ...
written 5 days ago by
Barry Digby • 250
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... Thank you for the clarification :) ...
written 6 days ago by
Barry Digby • 250
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... Hi,
I want to ask is it appropriate to generate a `tx2gene` file from an ENSEMBL cDNA reference file for bustools input?
I want to insert this code into a larger nextflow `kallisto | bustools` scRNA script so it will generate a `tx2gene` file for the analysis, flexible to different reference gen ...
written 6 days ago by
Barry Digby • 250
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... Thanks Pierre, just the guy I was hoping would see this question. Your suggestion worked.
Was my code using the GTF file once in the final process, and then ending? This seems to be the behaviour if i set the input GTF as ```files(params.annotation)```.
...
written 12 days ago by
Barry Digby • 250
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