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23 results • Page
1 of 1
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Rank
Views
Votes
Replies
0
votes
0
replies
32
views
DIFFBIND boxplot results, p value not significant
ChIP-seq
DiffBind
2 hours ago by
RD
▴ 10
0
votes
2
replies
87
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
2 hours ago by
ezz3
• 0
0
votes
4
replies
116
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
3 hours ago by
shpak.max
▴ 50
0
votes
1
reply
71
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 4 hours ago by
GenoMax
142k • written 5 hours ago by
s
• 0
1
vote
1
reply
62
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
4 hours ago by
Tuấn Anh
• 0
0
votes
2
replies
131
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
8 hours ago by
Shukai
• 0
0
votes
0
replies
53
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 9 hours ago by
GenoMax
142k • written 9 hours ago by
LuciaNhu
• 0
1
vote
2
replies
130
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
fasta
vcf
gene
updated 7 hours ago by
Ram
44k • written 10 hours ago by
Harshita
• 0
2
votes
0
replies
61
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
csaw
updated 5 hours ago by
Ram
44k • written 10 hours ago by
Rafael Soler
★ 1.2k
0
votes
0
replies
60
views
How does Kraken2 deal with poor read qualities?
kraken
qiime2
kraken2
qiime
updated 9 hours ago by
GenoMax
142k • written 10 hours ago by
Christopher
• 0
0
votes
1
reply
87
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 10 hours ago by
DBScan
▴ 300 • written 11 hours ago by
brunomiwa
• 0
0
votes
0
replies
56
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
11 hours ago by
Ayda Ecem
• 0
0
votes
3
replies
117
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 5 hours ago by
Ram
44k • written 12 hours ago by
pirku
• 0
0
votes
0
replies
59
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
15 hours ago by
Yao
▴ 30
0
votes
0
replies
65
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
17 hours ago by
dawnyipingzou
• 0
0
votes
4
replies
197
views
Where to find old version of GATK best practice
gatk
8 hours ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
91
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 17 hours ago by
Pierre Lindenbaum
161k • written 18 hours ago by
Peter Chung
▴ 200
0
votes
1
reply
103
views
CreateSeuratObject taking very long
seurat
updated 12 hours ago by
Nitin Narwade
★ 1.6k • written 21 hours ago by
eae6d2e7
• 0
0
votes
2
replies
172
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
11 hours ago by
Bjorn
• 0
0
votes
1
reply
123
views
vcf phasing
beagle
WhatsHap
phasing
updated 13 hours ago by
WouterDeCoster
47k • written 1 day ago by
safeassli
▴ 10
1
vote
2
replies
380
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 6 hours ago by
finch
• 0 • written 3 months ago by
star
▴ 10
1
vote
6
replies
358
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
13 hours ago by
Umer
▴ 50
0
votes
3
replies
237
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 52 minutes ago by
Nyksubuz
▴ 20 • written 5 days ago by
Luqman
• 0
23 results • Page
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Recent Votes
Comment: NGS forensics: how to know if data is fabricated
T2T-CHM13 "complete" human genome gff/gtf annotation file
Answer: T2T-CHM13 "complete" human genome gff/gtf annotation file
Comment: Problem in getting geo file through GEOQUERY
Answer: Problem in getting geo file through GEOQUERY
Comment: SnpEff and Snpsift
Comment: Problem in getting geo file through GEOQUERY
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Recent Awards •
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Scholar
to
Mathew
▴ 150
Popular Question
to
anasjamshed
▴ 120
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to
liyong
▴ 80
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Ashutosh Pandey
12k
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natasha.sernova
★ 4.0k
Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 20
Could share some examples for gene_ids?
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
yeah but i am unable to find the link of GPL6244.soft.gz
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 …
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