3 minutes ago by
dxj294
•
0
0
votes
0
replies
4
views
0
votes
0
replies
7
views
24 minutes ago by
evan.kransdorf
•
0
5
votes
5
replies
53
views
1
vote
1
reply
57
views
updated 2 hours ago by
ATpoint
87k
•
written 2 hours ago by
lea.preuss
•
0
0
votes
0
replies
44
views
8
votes
11
replies
252
views
0
votes
0
replies
36
views
0
votes
1
reply
125
views
updated 9 hours ago by
Meeru
•
0
•
written 1 day ago by
Physalia-courses
★
2.6k
836
votes
167
replies
174k
views
111 follow
updated 12 days ago by
Biostar
3.5k
•
written 8.4 years ago by
Istvan Albert
102k
0
votes
1
reply
103
views
updated 16 hours ago by
GenoMax
150k
•
written 16 hours ago by
himanshu0102
•
0
2
votes
2
replies
1.3k
views
4
votes
4
replies
207
views
0
votes
5
replies
234
views
updated 23 hours ago by
GenoMax
150k
•
written 1 day ago by
theresia.celine
•
0
1
vote
0
replies
125
views
10 minutes ago by
Ariadna
▴
30
3
votes
5
replies
246
views
0
votes
1
reply
155
views
1
vote
3
replies
1.7k
views
1
vote
5
replies
1.0k
views
updated 1 day ago by
GenoMax
150k
•
written 3.1 years ago by
biology_inform
▴
50
6
votes
3
replies
904
views
updated 1 day ago by
ehaag
▴
20
•
written 4.6 years ago by
rakinitopo
▴
10
0
votes
1
reply
259
views
0
votes
0
replies
102
views
0
votes
2
replies
195
views
updated 1 day ago by
ATpoint
87k
•
written 1 day ago by
leranwangcs
▴
150
1
vote
3
replies
648
views
2
votes
2
replies
199
views
updated 1 day ago by
Jorge - Ensembl
▴
20
•
written 1 day ago by
gernophil
▴
120
5
votes
5
replies
306
views
0
votes
2
replies
163
views
2
votes
4
replies
257
views
2 days ago by
SomeOne
▴
170
0
votes
0
replies
118
views
2 days ago by
ylkim9
•
0
0
votes
1
reply
141
views
updated 2 days ago by
GenoMax
150k
•
written 2 days ago by
AlmuhayyaA
•
0
1
vote
3
replies
254
views
updated 1 day ago by
ATpoint
87k
•
written 2 days ago by
pipelinfections
•
0
1
vote
0
replies
153
views
0
votes
3
replies
308
views
0
votes
1
reply
181
views
8
votes
18
replies
3.1k
views
8 follow
updated 2 days ago by
jena
▴
320
•
written 19 months ago by
fishingline37
•
0
1
vote
2
replies
244
views
updated 2 days ago by
dsull
★
7.4k
•
written 2 days ago by
marc.zimmerli
▴
10
0
votes
0
replies
154
views
2
votes
5
replies
643
views
1
vote
1
reply
211
views
1
vote
3
replies
276
views
updated 13 hours ago by
Jordan M Eizenga
▴
700
•
written 3 days ago by
Pau
•
0
0
votes
0
replies
149
views
3 days ago by
frarodmar17
•
0
0
votes
3
replies
424
views
1
vote
2
replies
256
views
1
vote
2
replies
303
views
3 days ago by
RJDan
•
0
0
votes
3
replies
846
views
4
votes
0
replies
238
views
0
votes
4
replies
317
views
0
votes
0
replies
257
views
1
vote
10
replies
1.1k
views
updated 1 day ago by
Mensur Dlakic
★
29k
•
written 6 days ago by
Sib
▴
60
0
votes
0
replies
245
views
1
vote
1
reply
386
views
updated 4 days ago by
Michael
55k
•
written 7 days ago by
Chatchapon
•
0
Recent Locations •
All
UCLA, 1 minute ago
United States, 3 minutes ago
Stony Brook University, NY, 4 minutes ago
Belgium, Brussels, 7 minutes ago
Norway stands with Ukraine, 7 minutes ago
Portugal, 10 minutes ago
United Kingdom, 11 minutes ago
Recent Awards •
All
Popular Question to
dxj294
•
0
Supporter to
b.contreras.moreira
▴
450
Popular Question to
Sam
▴
10
Popular Question to
AIMAR
•
0
Popular Question to
priya.bmg
▴
70
Recent Replies
Comment: Pre-Made STAR Index for mm10 Mouse Genome
by
Nerelys
•
0
Yes, I will consider that also. Thanks a lot!
Comment: Pre-Made STAR Index for mm10 Mouse Genome
by
GenoMax
150k
> as I do not have sufficient resources to generate the index myself.
If that is the case you may also run into issues with alignments. ST…
Comment: Pre-Made STAR Index for mm10 Mouse Genome
by
dsull
★
7.4k
Darn it lol! Think you beat me by a second!
Answer: Pre-Made STAR Index for mm10 Mouse Genome
by
dsull
★
7.4k
Found this online :)
http://refgenomes.databio.org/v3/assets/splash/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/star_index?tag=defa…
Comment: STAR vs. Kallisto
by
dsull
★
7.4k
Of course! Oh, the parameter is --d-list. By default, in `kb ref`, --d-list is set to whatever FASTA you supply to `kb ref` but you can dis…
Comment: STAR vs. Kallisto
by
gogeni5529
▴
60
thanks @delaneyksull for the comprehensive responses both in the answer as well as in the comments. I appreciate the time.
A comment to y…
Comment: STAR vs. Kallisto
by
dsull
★
7.4k
Also, this isn't arguing for/against kallisto. You're mentioning situations about ALIGNMENT issues; this is a QUANTIFICATION issue.
Comment: STAR vs. Kallisto
by
dsull
★
7.4k
A ton of benchmarking (across many papers) has already been done to show which tools perform best when. The literature has a ton of evidenc…
Comment: The volcano plot shows data with an arm-shaped enrichment.
by
ATpoint
87k
Usually odd shapes in these sorts of plots come from insufficient prefiltering. Here, in your `keep` all you do is to make sure that the ge…
Comment: STAR vs. Kallisto
by
ATpoint
87k
Unless you comprehensively show that one tool performs globally better and reveals more meaningful biology than the other the choice is in …
Comment: STAR vs. Kallisto
by
dsull
★
7.4k
After re-reading this, I'm going to push back against this answer a bit. In this case, it's 100% clear that pseudoalignment is producing th…
Comment: Is there a tool to obtain GO terms for thousands of genes at once?
by
GenoMax
150k
GeneSCF may be an option: https://github.com/genescf/GeneSCF?tab=readme-ov-file#Step-by-step-instructions
Please be aware that use of KEGG…
Comment: STAR vs. Kallisto
by
dsull
★
7.4k
On the contrary, I think the right approach is to test each tool and see where the difference arises :) -- papers would be much more inform…
Comment: STAR vs. Kallisto
by
ATpoint
87k
I use salmon-tximport/lengthScaledTPM-limma most of the time but other combinations work fine as well.
Traffic: 3584 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