44 minutes ago by
nicole.kavanagh
•
0
8
votes
9
replies
320
views
6 follow
0
votes
6
replies
298
views
updated 1 hour ago by
GenoMax
142k
•
written 22 days ago by
eesiribloom
▴
80
0
votes
6
replies
408
views
17 hours ago by
kl
▴
10
5
votes
5
replies
127
views
updated 1 hour ago by
atharvakarkare14
▴
30
•
written 4 hours ago by
Begonia_pavonina
▴
150
0
votes
5
replies
313
views
0
votes
4
replies
64
views
updated 42 minutes ago by
jared.andrews07
★
16k
•
written 1 hour ago by
JH
•
0
0
votes
4
replies
208
views
27 minutes ago by
matteo.levorato
•
0
1
vote
4
replies
1.0k
views
5
votes
4
replies
313
views
1
vote
3
replies
247
views
updated 21 hours ago by
ATpoint
82k
•
written 1 day ago by
jagdish7921
•
0
1
vote
2
replies
125
views
updated 7 hours ago by
ATpoint
82k
•
written 13 hours ago by
poordumbsillyidiot
•
0
1
vote
2
replies
209
views
10 hours ago by
rianna.collins
•
0
1
vote
2
replies
196
views
0
votes
1
reply
163
views
updated 21 hours ago by
Adam
▴
30
•
written 2 days ago by
Ahiad Chen Zion
•
0
0
votes
1
reply
76
views
1
vote
1
reply
63
views
0
votes
1
reply
170
views
0
votes
1
reply
158
views
0
votes
1
reply
25
views
1
vote
1
reply
58
views
updated 32 minutes ago by
jared.andrews07
★
16k
•
written 5 hours ago by
Oburah
•
0
0
votes
1
reply
56
views
0
votes
1
reply
155
views
1
vote
1
reply
79
views
updated 2 minutes ago by
Ram
43k
•
written 6 hours ago by
marco.barr
▴
90
0
votes
1
reply
540
views
0
votes
1
reply
740
views
0
votes
1
reply
101
views
updated 21 hours ago by
Ram
43k
•
written 23 hours ago by
ernestine.kubi
•
0
0
votes
1
reply
226
views
updated 11 hours ago by
Scooter
▴
280
•
written 6 days ago by
avocado123
•
0
0
votes
0
replies
1
view
just now by
Arun Sai Kumar
•
0
0
votes
0
replies
57
views
0
votes
0
replies
83
views
0
votes
0
replies
50
views
12 hours ago by
James
▴
10
0
votes
0
replies
46
views
0
votes
0
replies
34
views
0
votes
0
replies
34
views
1
vote
0
replies
182
views
5 hours ago by
carlopecoraro2
★
2.5k
0
votes
0
replies
6
views
0
votes
0
replies
39
views
updated just now by
Ram
43k
•
written 5 hours ago by
carlopecoraro2
★
2.5k
0
votes
0
replies
54
views
0
votes
0
replies
71
views
Recent Votes
Recent Locations •
All
Italy, just now
Indiana University, just now
United Kingdom, just now
United States, 1 minute ago
Russia, 2 minutes ago
United States, 3 minutes ago
United Kingdom, 3 minutes ago
Recent Awards •
All
Popular Question to
hafiz.talhamalik
▴
350
Popular Question to
Hayler Edu
▴
40
Popular Question to
eesiribloom
▴
80
Popular Question to
g.persic1991
•
0
Popular Question to
massa.kassa.sc3na
▴
600
Teacher to
shenwei356
8.5k
Popular Question to
Apex92
▴
280
Recent Replies
Comment: Do I need to go back and filter my long-reads?
by
Ram
43k
Do not delete posts that have received feedback. Engage with the user providing you feedback.
Answer: Download eQTL data of one specific gene for all tissues from GTEx
by
bk11
★
2.4k
Please kindly check your result here. You can click `csv` and download the date in this [link][1].
**OR**
If you prefer to use R, there i…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
matteo.levorato
•
0
but why not a single matrix with the 3 different condition and then by lfcShrink function get the DEGs of each condition?
Answer: Super ehancers
by
jared.andrews07
★
16k
Sure, you can run it on them. Stitching tends to happen less frequently since the ATAC peaks are generally less wide than H3K27ac, but it'l…
Answer: What purposes can TPM values be used for?
by
jared.andrews07
★
16k
TPMs cannot be used for intersample comparisons, but they can be used for intrasample comparisons (e.g. comparing relative expression level…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
•
0
Thank you so much for the recommendation and the very clear explanation , it's much appreciated. I have already made core-gene phylogenies/…
Comment: What purposes can TPM values be used for?
by
Adam
▴
30
Have you run FASTQC and checked the mapping efficiency of WT3?
> would running DESeq using TPM values help solve my problem?
No, DESeq sh…
Answer: How goes gene length effect the number of reads mapped
by
i.sudbery
19k
See my answer about the what hows and whens of RNA-seq normalisation here:
https://www.biostars.org/p/9586553/#9586566
Comment: What purposes can TPM values be used for?
by
dsull
★
5.9k
Since you have mutant vs wild-type, using DESeq2 is the right thing to do. Rather than showing a small table of numbers, you should make a …
Answer: What purposes can TPM values be used for?
by
i.sudbery
19k
See my post here for more details on RNA-seq normalisation:
https://www.biostars.org/p/9586553/#9586566
In short, TPM normalises for ge…
Comment: Bacterial plasmid analysis
by
Zamin Iqbal
▴
10
I vote for this, it's the best! (but also, I am Daria's PhD supervisor so I am biased). Preprint out soon(ish) [no pressure Daria!]
Comment: Downsampling long-read BAM files
by
GenoMax
142k
Is this what you used ultimately? Did this tool satisfy the "specific average depth" requirement?
You could accept (green check mark) this…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
Estevão
•
0
Thank you. My budget is around 20 thousand dollars.
Answer: Problem with data downloaded from Short Reads Archive (SRA)
by
atharvakarkare14
▴
30
Prefetch files using sratoolkit **prefetch** command and then use **fasterq-dump**. There you can see the number of reads. For validation, …
Answer: Downsampling long-read BAM files
by
eesiribloom
▴
80
random downsampling of bam files is now possible using [rasusa][1] [v1.0.0][2] with the `aln` subcommand
[1]: https://github.com/mbh…
Traffic: 3076 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