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Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
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C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
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How can I perform Differential expression analysis with just one control and one cancer sample?
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ATpoint
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What is your question? It's unclear.
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One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Gordon Smyth
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See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Our resul…
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txema.heredia
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Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
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Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
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hophuquy0944
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i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
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Yes, `bedmap` will perform operations on one or two BED files.
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Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
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Ngrin
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Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
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This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
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Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
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bk11
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You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
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I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
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There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
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