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Whither my badges?
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Comment: Unusual FASTQ file
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Ram
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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…
Comment: How to make a dotplot for bulk RNA average expression ?
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bhumm
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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…
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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Vincent Laufer
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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?
Answer: Make a BedGraph file
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bhumm
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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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ATpoint
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STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline
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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…
Comment: RNAseq Data and Pipeline
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Ram
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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…
Comment: RNAseq Data and Pipeline
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Ram
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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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turcoa1
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```r
query <- GDCquery(
project = "TCGA-THCA",
data.category = "Transcriptome Profiling",
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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ashleymb1116
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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…
Comment: Salmon Index
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> I am using the Bos Taurus files
Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
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