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59 results • Page
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0
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97
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pseudo-bulk
scRNAseq
DE
updated 3 hours ago by
Ram
39k • written 21 days ago by
safeassli
• 0
0
votes
0
replies
128
views
Per base sequence content warning in ChIPseq data FastQC analysis
ChIP-seq
FastQC
updated 3 hours ago by
Ram
39k • written 4 weeks ago by
shashianand15
• 0
0
votes
0
replies
1.1k
views
EDGE microarray time series analysis fit_models() ERROR
microarray
time-series
updated 6 hours ago by
Ram
39k • written 5.4 years ago by
tleona3
▴ 10
0
votes
0
replies
184
views
Bed files of narrowPeak in ENCODE
ENCODE
updated 3 hours ago by
Ram
39k • written 25 days ago by
younglin113
▴ 50
0
votes
0
replies
1.3k
views
Cuffdiff with 2 conditions and time series
cuffdiff
time-series
RNA-Seq
transcriptome
updated 6 hours ago by
Ram
39k • written 6.2 years ago by
KL
• 0
0
votes
0
replies
930
views
Where can I find, which yeast genes definitely have similar functions?
gene
functional-genomics
RNA-Seq
time-series
updated 6 hours ago by
Ram
39k • written 6.2 years ago by
Thomas.F.Hahn3
▴ 30
0
votes
0
replies
639
views
time Course RNa-seq data from peripheral blood
time-course
RNA-Seq
updated 8 hours ago by
Ram
39k • written 4.0 years ago by
sabaghianamir70
▴ 70
0
votes
0
replies
794
views
Simulating Time Course RNA-Seq Data With Polyester
Time-Course
RNA-Seq
updated 8 hours ago by
Ram
39k • written 3.9 years ago by
eashby47
▴ 10
0
votes
0
replies
639
views
What option should I use for show me result which I can filter my data by their p-value and FC?
MASIGPRO
Time-Course
RNA-Seq
updated 8 hours ago by
Ram
39k • written 3.4 years ago by
sabaghianamir70
▴ 70
59 results • Page
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Answer: How do you add an ORF that overlaps the two regions where a circular genome is c
C: PLINK logistic regression analysis and covariates
Comment: Regular Expression for conversion
Answer: RNAseq Data and Pipeline
Comment: Salmon Index
Comment: Salmon Index
Resequencing data of pangenome
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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
▴ 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
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
▴ 40
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
72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline
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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
• 0
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
39k
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
129k
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
• 0
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 …
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