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Recent Replies
Answer: What is the best way to clean bulk RNA-seq data?
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swbarnes2
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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?
https://bedtools.readthedocs.io/en/latest/content/tools/window.html
https://bedtools.readthedocs.io…
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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…
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```r
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data.type = "Gene Expression Quantificatio…
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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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I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
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> I am using the Bos Taurus files
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Thank you, yes I am using the newer version of Ensembl. Above with Arabidopsis is the example Salmon gave, I am using the Bos Taurus files.…
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Show us your exact cellranger and STARsolo commands, the full output to STARsolo as well as your thoughts on why it's not working for you.
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