updated 2.2 years ago by
Silvia Prieto
▴
30
•
written 2.2 years ago by
kylakell
•
0
0
votes
5
replies
1.5k
views
0
votes
0
replies
444
views
updated 2.2 years ago by
Ram
45k
•
written 2.2 years ago by
sahalpaladan
▴
10
1
vote
1
reply
917
views
updated 2.2 years ago by
Ram
45k
•
written 2.2 years ago by
Researcher
▴
20
0
votes
3
replies
1.1k
views
updated 2.2 years ago by
Matthias Zepper
5.1k
•
written 2.2 years ago by
Maliha
▴
30
0
votes
0
replies
525
views
updated 2.2 years ago by
Ram
45k
•
written 2.2 years ago by
ijlal.hyder2012
▴
20
3
votes
16
replies
3.3k
views
updated 23 months ago by
Brian Bushnell
20k
•
written 2.3 years ago by
berndmann
▴
10
4
votes
6
replies
7.6k
views
updated 2.2 years ago by
Ram
45k
•
written 13.7 years ago by
boczniak767
▴
880
0
votes
0
replies
376
views
updated 2.2 years ago by
colindaven
8.0k
•
written 2.2 years ago by
megoo
•
0
0
votes
0
replies
1.1k
views
2.2 years ago by
kenneditodd
▴
50
1
vote
2
replies
1.4k
views
3
votes
1
reply
1.4k
views
updated 2.2 years ago by
Nitin Narwade
★
1.7k
•
written 2.2 years ago by
safeassli
▴
10
0
votes
3
replies
1.7k
views
0
votes
2
replies
807
views
1
vote
2
replies
1.1k
views
2.2 years ago by
Chris Dean
▴
420
0
votes
0
replies
515
views
2.2 years ago by
pablo
▴
350
0
votes
5
replies
1.3k
views
updated 2.2 years ago by
Trivas
★
1.9k
•
written 2.2 years ago by
waqasnayab
▴
250
1
vote
2
replies
1.1k
views
2.2 years ago by
HK
▴
40
1
vote
1
reply
932
views
updated 2.2 years ago by
Nitin Narwade
★
1.7k
•
written 2.2 years ago by
Aki
▴
20
0
votes
6
replies
2.7k
views
updated 13 months ago by
Yan
•
0
•
written 2.2 years ago by
g744695539
•
0
4
votes
1
reply
1.2k
views
updated 2.2 years ago by
Nitin Narwade
★
1.7k
•
written 2.2 years ago by
Manuel Sokolov Ravasqueira
▴
110
0
votes
0
replies
474
views
6
votes
7
replies
1.3k
views
2
votes
3
replies
1.1k
views
12
votes
7
replies
5.0k
views
4
votes
6
replies
1.7k
views
0
votes
2
replies
707
views
2.2 years ago by
Parker.Payne
•
0
4
votes
2
replies
2.2k
views
Tutorial:
How to use UCSC genome browser to check the transcription factor binding at your favorite gene
2.2 years ago by
Ming Tommy Tang
★
4.7k
0
votes
1
reply
1.1k
views
updated 2.2 years ago by
Ming Tommy Tang
★
4.7k
•
written 2.2 years ago by
은서
•
0
0
votes
2
replies
1.3k
views
updated 2.2 years ago by
Jesse
▴
880
•
written 2.2 years ago by
j.gleixner
▴
30
0
votes
2
replies
2.5k
views
3
votes
8
replies
2.3k
views
2.2 years ago by
Apprentice
▴
190
2
votes
4
replies
1.8k
views
2.2 years ago by
anikcropscience
▴
270
0
votes
2
replies
1.1k
views
0
votes
2
replies
1.1k
views
2.2 years ago by
dalibenam64
•
0
0
votes
1
reply
586
views
0
votes
3
replies
1.0k
views
0
votes
0
replies
409
views
4
votes
3
replies
1.3k
views
13
votes
6
replies
42k
views
8
votes
7
replies
4.5k
views
7 follow
updated 2.2 years ago by
Hugo
▴
400
•
written 3.6 years ago by
b.shrestha
▴
10
4
votes
3
replies
2.5k
views
updated 2.2 years ago by
DareDevil
★
4.4k
•
written 2.2 years ago by
fishingline37
•
0
1
vote
1
reply
697
views
0
votes
1
reply
1.8k
views
updated 2.2 years ago by
Ram
45k
•
written 2.2 years ago by
pairedttest
▴
40
2
votes
4
replies
1.2k
views
0
votes
0
replies
412
views
2
votes
3
replies
1.9k
views
3
votes
2
replies
1.2k
views
2.2 years ago by
Rob
▴
180
0
votes
1
reply
739
views
3
votes
4
replies
1.8k
views
updated 2.2 years ago by
Eric Lim
★
2.2k
•
written 2.2 years ago by
rhonddaskl
•
0
4
votes
9
replies
2.2k
views
updated 2.2 years ago by
glenn.hickey
▴
550
•
written 2.2 years ago by
Maxine
▴
50
Recent Votes
Recent Locations •
All
Canada, just now
United States, just now
Chile, 4 minutes ago
France/Nantes/Institut du Thorax - INSERM UMR1087, 6 minutes ago
Germany, 11 minutes ago
United States, 13 minutes ago
United States, 15 minutes ago
Recent Awards •
All
Popular Question to
Apprentice
▴
190
Scholar to
yura.grabovska
▴
830
Popular Question to
Assa Yeroslaviz
★
1.9k
Popular Question to
DdogBoss
▴
20
Popular Question to
curious
▴
890
Popular Question to
Juke34
9.3k
Popular Question to
DBScan
▴
530
Recent Replies
Comment: how to respond that my research does not have experimental validation
by
ATpoint
89k
You should give the reviewer something. An independent way of in silico validation, other supporting analysis. Just "no" might lead to reje…
Answer: Which aligner is more suitable for ONT R10.4.1 Dorado-corrected reads: minimap2
by
okiedokie1208
▴
40
I believe ONT recommends Minimap2. This is also the default tools in their EPI2ME workflow.
Comment: how to respond that my research does not have experimental validation
by
rfran010
★
1.7k
Yes, and if you are going to mention that experimental validation is not possible or outside the scope of your paper, kindly remind the rev…
Comment: Errors with RSEM/bowtie2
by
GenoMax
154k
Is it possible that mismatched R1/R2 files were used in one of the steps?
If you are sure that has not happened then you could try to see…
Comment: Quantification using salmon in alignment-based mode after minimap2 run
by
GenoMax
154k
In case you were not aware ONT also provides a transcriptome workflow for long reads: https://github.com/epi2me-labs/wf-transcriptomes
Comment: how to respond that my research does not have experimental validation
by
ATpoint
89k
Either do experimental validation, or say that not possible due to lack of collaboration, infrastructure, lab background. If they reject, s…
Answer: Quantification using salmon in alignment-based mode after minimap2 run
by
Rob
7.1k
As @atpoint suggests, you must align against the transcriptome. Also, the other relevant flags should be set (i.e. `--secondary=no` will di…
Answer: Quantification using salmon in alignment-based mode after minimap2 run
by
ATpoint
89k
Yes, must strictly be transcriptome. Reference from developer: https://www.biostars.org/p/9556364/
Comment: Errors with RSEM/bowtie2
by
Olivia
•
0
Yes, they removed the adapters, so I did not have to do extra steps for this (other than Trimmomatic within Trinity to get rid of short con…
Answer: infercnv error at STEP 18 - file descriptor is too large for select()
by
yura.grabovska
▴
830
Noticed that running `infercnv::CreateInfercnvObject()` generates a warning:
```
WARN [2025-10-06 14:43:38] Please use "options(scipen = …
Comment: Which aligner is more suitable for ONT R10.4.1 Dorado-corrected reads: minimap2
by
tungsega
▴
10
Thank you for your reply.
I’m currently trying to perform alignments using both aligners, but I wanted to ask if anyone has conducted a si…
Comment: Which aligner is more suitable for ONT R10.4.1 Dorado-corrected reads: minimap2
by
colindaven
8.0k
Good summary. I never tried winnowmap despite it's apparent advantages. If you have really repeat rich regions like centromeres that it may…
Comment: Need Help : JGI IMG Bulk Download
by
GenoMax
154k
Please post direct links to software you mention. Not sure why you are using LinkedIn short URL's.
Historically downloads from JGI have be…
Comment: Hifiasm is getting killed while trying to assemble a genome
by
pranavdatar01
•
0
This is the paper: https://doi.org/10.3389/fevo.2022.850817 (Genome of Varanus salvator macromaculatus (Asian Water Monitor) Reveals Adapta…
Comment: How to create a consensus of a contig with samtools or bbmap?
by
lieven.sterck
16k
great to hear!
and yes, spades in stead of samtools makes much more sense :-)
Traffic: 3353 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