0
votes
0
replies
14
views
0
votes
2
replies
43
views
0
votes
4
replies
63
views
54 minutes ago by
shpak.max
▴
50
0
votes
1
reply
45
views
1
vote
1
reply
55
views
2 hours ago by
Tuấn Anh
•
0
0
votes
2
replies
127
views
0
votes
0
replies
49
views
1
vote
2
replies
123
views
2
votes
0
replies
55
views
updated 3 hours ago by
Ram
44k
•
written 7 hours ago by
Rafael Soler
★
1.2k
0
votes
0
replies
55
views
0
votes
1
reply
84
views
0
votes
0
replies
53
views
9 hours ago by
Ayda Ecem
•
0
0
votes
3
replies
113
views
0
votes
0
replies
56
views
0
votes
0
replies
62
views
0
votes
4
replies
189
views
5 hours ago by
Zhenyu Zhang
★
1.2k
0
votes
1
reply
88
views
updated 15 hours ago by
Pierre Lindenbaum
161k
•
written 15 hours ago by
Peter Chung
▴
200
0
votes
1
reply
100
views
updated 10 hours ago by
Nitin Narwade
★
1.6k
•
written 19 hours ago by
eae6d2e7
•
0
0
votes
2
replies
168
views
9 hours ago by
Bjorn
•
0
0
votes
1
reply
119
views
updated 10 hours ago by
WouterDeCoster
47k
•
written 1 day ago by
safeassli
▴
10
1
vote
2
replies
378
views
Recent Votes
Recent Locations •
All
USA, just now
United States, 1 minute ago
Brazil, 2 minutes ago
Germany, 2 minutes ago
ETH Zurich, 3 minutes ago
Australia, 4 minutes ago
Turkey, 7 minutes ago
Recent Awards •
All
Popular Question to
anasjamshed
▴
120
Popular Question to
liyong
▴
80
Scholar to
Ashutosh Pandey
12k
Popular Question to
O.rka
▴
720
Popular Question to
natasha.sernova
★
4.0k
Popular Question to
Picasa
▴
640
Recent Replies
Comment: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
> Can you send me ftp link so I can download that soft file manually?
Please find this link on your own by browsing the respective GEO ent…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴
120
Thanks . I have downloaded all other files but just have problem in
Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE)…
Answer: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
ezz3
•
0
Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
Answer: Multi-ploid data in ANGSD and NGSadmix
by
andersdetermig
▴
20
1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
Pierre Lindenbaum
161k
"Are you using correct reference?"
may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴
50
Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
Answer: Add stats to the plot
by
Ghada
•
0
It works. I have added this code
my_comparisons=list(c("HRSV", "HRSV_RBV"))
plot + stat_compare_means(method = "wilcox.test",comparis…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
LChart
3.9k
I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴
120
Basically this is my code:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
#
# pkgs <- rowna…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴
50
If that were the case, I would expect there not to be any uncalled sites in the vcf, yet there are a large number of sites with "." placeho…
Comment: Problem in getting geo file through GEOQUERY
by
bk11
★
2.5k
It just runs fine for me with just a single line of code.
library(GEOquery)
GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE)
…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
Dave Carlson
★
1.7k
I can't speak to UnifiedGenotyper, as it has been many years since GATK stopped supporting it, and I have not used it in a long time. But …
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴
120
I want to get lot of files through code
Comment: Problem in getting geo file through GEOQUERY
by
GenoMax
142k
Query seems to be timing out. Try getting the file directly here: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1145/matrix/GSE1145-GP…
Traffic: 2235 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