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Recent Replies
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
by
swbarnes2
13k
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
by
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
by
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
by
turcoa1
•
0
```r
query <- GDCquery(
project = "TCGA-THCA",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree
by
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.
Comment: RNAseq Data and Pipeline
by
Ram
39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index
by
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
by
GenoMax
129k
> I am using the Bos Taurus files
Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
Comment: Salmon Index
by
ashleymb1116
•
0
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.…
Comment: Query qbout single cell sequencing
by
Ram
39k
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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