0
votes
0
replies
159
views
0
votes
0
replies
151
views
0
votes
0
replies
143
views
0
votes
2
replies
265
views
0
votes
1
reply
193
views
updated 4 days ago by
Vincent Laufer
★
2.8k
•
written 5 days ago by
Saran
▴
20
1
vote
1
reply
162
views
0
votes
1
reply
140
views
1
vote
2
replies
215
views
4 days ago by
Prangan
▴
20
0
votes
0
replies
106
views
0
votes
2
replies
189
views
4 days ago by
manaswiniparija3
▴
10
0
votes
4
replies
273
views
3
votes
5
replies
342
views
1
vote
2
replies
235
views
0
votes
1
reply
151
views
0
votes
3
replies
249
views
5 days ago by
ethan.kreuzer
•
0
2
votes
3
replies
258
views
6 days ago by
erik.burchard
▴
10
0
votes
0
replies
110
views
1
vote
2
replies
277
views
0
votes
1
reply
182
views
1
vote
4
replies
341
views
updated 2 days ago by
solarchan7
•
0
•
written 7 days ago by
survive
•
0
3
votes
6
replies
537
views
6 days ago by
Sowmya Pulapet
▴
30
0
votes
2
replies
355
views
0
votes
0
replies
192
views
7
votes
12
replies
840
views
0
votes
0
replies
97
views
0
votes
0
replies
184
views
updated 2 hours ago by
Ram
39k
•
written 25 days ago by
younglin113
▴
50
0
votes
4
replies
322
views
0
votes
0
replies
128
views
updated 2 hours ago by
Ram
39k
•
written 4 weeks ago by
shashianand15
•
0
0
votes
4
replies
499
views
6 days ago by
Begonia_pavonina
▴
100
0
votes
3
replies
452
views
0
votes
5
replies
697
views
1
vote
0
replies
442
views
updated 7 hours ago by
Ram
39k
•
written 17 months ago by
jennifer.conrad84
▴
10
2
votes
6
replies
999
views
0
votes
0
replies
456
views
updated 7 hours ago by
Ram
39k
•
written 2.5 years ago by
Omics data mining
▴
220
0
votes
0
replies
450
views
0
votes
0
replies
610
views
0
votes
4
replies
783
views
updated 7 hours ago by
Ram
39k
•
written 3.1 years ago by
donnieDarko
•
0
0
votes
1
reply
750
views
updated 7 hours ago by
Ram
39k
•
written 3.2 years ago by
donnieDarko
•
0
0
votes
0
replies
835
views
0
votes
0
replies
639
views
updated 7 hours ago by
Ram
39k
•
written 3.4 years ago by
sabaghianamir70
▴
70
0
votes
0
replies
794
views
0
votes
0
replies
639
views
updated 7 hours ago by
Ram
39k
•
written 4.0 years ago by
sabaghianamir70
▴
70
2
votes
0
replies
720
views
updated 1 hour ago by
Ram
39k
•
written 4.0 years ago by
nickvpinkham
▴
20
2
votes
3
replies
687
views
updated 1 hour ago by
Ram
39k
•
written 4.1 years ago by
cipri91rusu
•
0
0
votes
1
reply
800
views
updated 2 hours ago by
Ram
39k
•
written 4.1 years ago by
nesma.abdelaziz
•
0
0
votes
1
reply
847
views
updated 5 hours ago by
Ram
39k
•
written 4.2 years ago by
abhijit.synl
▴
60
3
votes
16
replies
9.9k
views
1
vote
10
replies
2.5k
views
0
votes
0
replies
989
views
0
votes
0
replies
1.5k
views
Recent Locations •
All
United States, 1 minute ago
United States, 1 minute ago
United States, 1 minute ago
United States, 3 minutes ago
Irbid, 4 minutes ago
United Kingdom, 4 minutes ago
United States, 7 minutes ago
Recent Awards •
All
Popular Question to
tarek.mohamed
▴
350
Popular Question to
carlopecoraro2
★
2.3k
Popular Question to
kamanovae
▴
80
Popular Question to
Lila M
★
1.2k
Popular Question to
oakhamwolf
▴
20
Commentator to
Istvan Albert
98k
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
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
•
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 …
Traffic: 2445 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6