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Recent Replies
Comment: Unusual FASTQ file
by
Ram
39k
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 ?
by
bhumm
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40
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?
by
swbarnes2
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There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
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
by
bhumm
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Bedtools window piped into genomecov?
https://bedtools.readthedocs.io/en/latest/content/tools/window.html
https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline
by
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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swbarnes2
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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
by
Ram
39k
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 …
Comment: RNAseq Data and Pipeline
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turcoa1
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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…
Comment: NCBI Common Taxonomy Tree
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GenoMax
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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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Ram
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What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index
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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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GenoMax
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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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