updated 6 hours ago by
Damianos P. Melidis
▴
40
•
written 6.5 years ago by
DanielC
▴
190
7
votes
7
replies
2.8k
views
0
votes
2
replies
144
views
0
votes
0
replies
78
views
837
votes
170
replies
178k
views
112 follow
updated 4 weeks ago by
Biostar
3.6k
•
written 8.5 years ago by
Istvan Albert
102k
0
votes
0
replies
69
views
0
votes
0
replies
286
views
updated 1 day ago by
GenoMax
151k
•
written 1 day ago by
salma.sarker
•
0
0
votes
0
replies
91
views
1 day ago by
xinguok794
•
0
1
vote
1
reply
359
views
updated 1 day ago by
LChart
4.9k
•
written 3 days ago by
anita.szabo08
▴
10
0
votes
2
replies
182
views
0
votes
3
replies
180
views
0
votes
1
reply
189
views
0
votes
1
reply
180
views
0
votes
1
reply
150
views
1
vote
3
replies
227
views
updated 2 days ago by
shelkmike
★
1.6k
•
written 2 days ago by
synthiiihuh
•
0
0
votes
1
reply
180
views
updated 2 days ago by
GenoMax
151k
•
written 2 days ago by
gil.hornung
▴
100
2
votes
4
replies
290
views
0
votes
2
replies
203
views
0
votes
1
reply
172
views
0
votes
1
reply
364
views
3
votes
1
reply
170
views
2
votes
4
replies
291
views
updated 13 hours ago by
Gordon Smyth
★
8.1k
•
written 2 days ago by
Nasim Gandomdoust
•
0
7
votes
3
replies
291
views
updated 1 day ago by
jared.andrews07
★
18k
•
written 2 days ago by
txema.heredia
▴
240
0
votes
0
replies
122
views
2 days ago by
Physalia-courses
★
2.6k
2
votes
3
replies
298
views
6
votes
12
replies
619
views
0
votes
12
replies
912
views
0
votes
0
replies
129
views
2
votes
3
replies
376
views
updated 3 days ago by
dariober
15k
•
written 4 days ago by
Matteo Ungaro
▴
120
3
votes
1
reply
284
views
0
votes
1
reply
175
views
updated 3 days ago by
GenoMax
151k
•
written 3 days ago by
nmannda148
•
0
4
votes
1
reply
215
views
0
votes
4
replies
338
views
4
votes
6
replies
439
views
0
votes
0
replies
159
views
3 days ago by
mickley413
•
0
1
vote
10
replies
2.0k
views
2
votes
4
replies
621
views
1
vote
2
replies
283
views
1
vote
2
replies
278
views
2 days ago by
yura.grabovska
▴
780
0
votes
0
replies
186
views
4 days ago by
Physalia-courses
★
2.6k
2
votes
5
replies
425
views
updated 2 days ago by
GenoMax
151k
•
written 4 days ago by
Assa Yeroslaviz
★
1.9k
3
votes
5
replies
467
views
updated 17 hours ago by
Mensur Dlakic
★
29k
•
written 5 days ago by
shevch2009
▴
20
0
votes
2
replies
314
views
4 days ago by
khp35
•
0
0
votes
0
replies
199
views
0
votes
1
reply
290
views
0
votes
0
replies
207
views
6
votes
3
replies
354
views
0
votes
1
reply
258
views
updated 4 days ago by
Pierre Lindenbaum
166k
•
written 4 days ago by
María José
▴
10
4
votes
7
replies
3.6k
views
updated 5 days ago by
Joel Wallenius
▴
220
•
written 4.9 years ago by
AR
•
0
2
votes
8
replies
688
views
2 days ago by
AIMAR
▴
10
2
votes
2
replies
321
views
updated 5 days ago by
Pierre Lindenbaum
166k
•
written 5 days ago by
María José
▴
10
Recent Votes
Recent Locations •
All
Norway stands with Ukraine, 2 minutes ago
United States, 15 minutes ago
UCLA, 15 minutes ago
Indonesia, 16 minutes ago
France, 23 minutes ago
Spain, 33 minutes ago
Bologna, 36 minutes ago
Recent Awards •
All
Popular Question to
Aki
▴
20
Popular Question to
Physalia-courses
★
2.6k
Popular Question to
Pierre Lindenbaum
166k
Popular Question to
Wenhai
•
0
Teacher to
jared.andrews07
★
18k
Popular Question to
Lélé
▴
10
Recent Replies
Comment: de novo chromosome level assembly
by
mthm
▴
80
I suppose the first one, since I don't have the information of the real chromosome
Answer: How to Identify the pathogenicity of a set of variants (by using ACMG guidelines
by
Damianos P. Melidis
▴
40
Dear DK,
Don't know if you are still interested in bioinformatics tools to implement ACMG but if you do let me share this biostars [post…
Comment: ACMG assignment tools
by
Damianos P. Melidis
▴
40
Hey, just to update with more tools:
- the wonderful* [TAPES][1]
- [vaRHC][2]
- [auto-acmg][3]
- genotoscope (see mark at the end)
Please…
Comment: Mass-spectrometry proteomics
by
Gordon Smyth
★
8.1k
limpa shares the full capabilities of the limma package, which includes adjustment for batch effects and outliers. To adjust for batch effe…
Comment: Why am I getting the exact same MarkDuplicates results when passing a query or
by
curious
▴
890
There are no secondary alignments as per :
samtools -f 0x100 {my_bam}
I only get secondary alignments if I add the `-a` flag to bwa …
Comment: Assemblers for short read bacterial isolates data
by
Mensur Dlakic
★
29k
Binning can be done in seconds, and there is no harm in trying it. If you run CheckM analyses before and after binning, it should give you …
Comment: Why am I getting the exact same MarkDuplicates results when passing a query or
by
GenoMax
151k
Can you provide the actual metrics output?
> What could be causing this?
Perhaps your data has no secondary/supplementary alignments.
Al…
Comment: Unsure whether or not I overcorrected for batch effect in dataset
by
Megan
▴
50
Thank you so much for the suggestion. I have included my code in the post.
Comment: Primer removal in amplicon sequencing
by
GenoMax
151k
`DADA2` pipeline states that all non-biological nucleotides need to be removed so choose accordingly: https://benjjneb.github.io/dada2/tuto…
Comment: Mass-spectrometry proteomics
by
Nasim Gandomdoust
•
0
Thank you for your reply. I would like to know if the package can handle batch effects and outlier samples too.
Answer: Which GWAS tool to use that can work on Czech cases and British controls, on a b
by
LChart
4.9k
There is really no way for you to do this analysis - having cases and controls perfectly confounded by populations means that every variant…
Comment: Unsure whether or not I overcorrected for batch effect in dataset
by
cfos4698
★
1.1k
It would help if you provided your code so others know what steps you took to batch-correct your data
Comment: Primer removal in amplicon sequencing
by
sxf520
•
0
Thanks. I actually want to know if I should use the full sequence (with the overhang part) or only the gene specific part as the primer se…
Comment: Primer removal in amplicon sequencing
by
GenoMax
151k
If you are looking to remove the primer sequences then you can provide these to scan/trim programs like `bbduk.sh` from BBMap suite or `fas…
Answer: GATK BQSR error — Reference and BAM file chromosome name mismatch (“chr” vs. no
by
Pierre Lindenbaum
166k
This question has been asked many times: https://www.biostars.org/p/9475152/ , https://www.biostars.org/p/146322/ , https://www.biostars.or…
Traffic: 2369 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