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Recent Replies
Answer: I don't want to believe the Interproscan DB estimated download time.
by
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With [**aria2**][1] and multiple connections, I download at ~2.2MiB. The estimate is still ~190 hours.
aria2c --continue=true --max-…
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if you want the genes in your count matrix use `rownames(obj)`. Or are you looking to get all genes with count > 0 for a particular cell? P…
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People from the middle east/indian subcontinent often associate the term "post title" with their job title, because a) post translates more…
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I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
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There really is no "best". Just find something reasonable, and document what you chose.
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ok interesting.
Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
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Bedtools window piped into genomecov?
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STAR counts are the raw counts, that is appropriate for DESeq2.
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STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
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There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
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my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
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Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline
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```r
query <- GDCquery(
project = "TCGA-THCA",
data.category = "Transcriptome Profiling",
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It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
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What data are you downloading? Can you show us your GDCquery commands please?
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