5.6 years ago by
anonymous1192976466
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15 days ago by
Rafael Soler
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updated 11.7 years ago by
Lars Juhl Jensen
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written 12.1 years ago by
Pri
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6.3 years ago by
statfa
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updated 5 months ago by
Ram
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written 7.9 years ago by
sarathkurichiyil
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updated 17 months ago by
Ram
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written 8.8 years ago by
trakhtenberg
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updated 5 months ago by
Ram
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written 8.0 years ago by
QVINTVS_FABIVS_MAXIMVS
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updated 21 months ago by
Ram
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written 3.4 years ago by
Begonia_pavonina
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5.0 years ago by
plebaninora
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updated 18 months ago by
ATpoint
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written 18 months ago by
suzanne rein
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5.3 years ago by
ishackm
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3.1 years ago by
lokeshp14cs24
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5.9 years ago by
Jokhe
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updated 7.0 years ago by
Biostar
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written 7.0 years ago by
12021560-040
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4.1 years ago by
williamsbrian5064
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2.4 years ago by
dare_devil
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9.3 years ago by
inadamj
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4.8 years ago by
marongiu.luigi
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5.1 years ago by
mhyunjunkang
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updated 14 months ago by
Ram
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written 14 months ago by
Confused_human
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updated 3.3 years ago by
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written 3.3 years ago by
gable_works
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7.2 years ago by
Gabe Anderson
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updated 9.5 years ago by
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written 10.2 years ago by
Ashutosh Pandey
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Recent Replies
Answer: What is the best way to clean bulk RNA-seq data?
by
swbarnes2
13k
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
★
2.8k
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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40
Bedtools window piped into genomecov?
https://bedtools.readthedocs.io/en/latest/content/tools/window.html
https://bedtools.readthedocs.io…
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by
ATpoint
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STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline
by
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
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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 …
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
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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
by
turcoa1
•
0
```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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by
Ram
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What data are you downloading? Can you show us your GDCquery commands please?
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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…
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by
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 …
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.…
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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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