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711 results • Page
3 of 15
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Views
Votes
Replies
6
votes
4
replies
376
views
Details on salmon index
Salmon
updated 4 days ago by
Rob
6.6k • written 5 days ago by
Lorenzo
• 0
0
votes
0
replies
163
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
5 days ago by
Jsarria.EEAD
• 0
0
votes
2
replies
268
views
How can I calculate the OS of each patient?
overall-survival
1 day ago by
Pedro
• 0
1
vote
1
reply
224
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 5 days ago by
Ram
44k • written 5 days ago by
m90
▴ 30
0
votes
0
replies
155
views
cat-bgen fail
bgenix
updated 5 days ago by
Ram
44k • written 5 days ago by
lambard
• 0
3
votes
4
replies
352
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 4 days ago by
Jeremy Leipzig
22k • written 5 days ago by
Ali
• 0
3
votes
3
replies
260
views
getting exon coordinates
genomics
updated 5 days ago by
Ram
44k • written 5 days ago by
Xbox_27
• 0
0
votes
4
replies
345
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 4 days ago by
Tony
• 0 • written 6 days ago by
vk
▴ 10
1
vote
5
replies
338
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 5 days ago by
Ram
44k • written 5 days ago by
manuelmourato25
• 0
3
votes
4
replies
430
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Pierre Lindenbaum
161k
2
votes
11
replies
770
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
4 days ago by
egascon
• 0
1
vote
1
reply
210
views
API kegg - IndexError: list index out of range
kegg
API
updated 4 days ago by
Nyksubuz
▴ 20 • written 5 days ago by
mirwa.zidi93
• 0
0
votes
0
replies
151
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
5 days ago by
Novogene
▴ 420
0
votes
0
replies
147
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
5 days ago by
ebertomeup
• 0
0
votes
3
replies
293
views
Sam file Header problem
Sam
Header
problem
file
updated 4 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
saifulislam99121
• 0
1
vote
3
replies
301
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 5 days ago by
Ram
44k • written 6 days ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
598
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 5 days ago by
valdirbarth
▴ 20 • written 13 months ago by
Salomé
• 0
0
votes
0
replies
151
views
select set of intervals that cover a genomic region
GRanges
bed
5 days ago by
ntsopoul
▴ 60
1
vote
1
reply
206
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 5 days ago by
Ram
44k • written 5 days ago by
dwpeng
▴ 10
0
votes
2
replies
225
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
1 day ago by
Luqman
• 0
2
votes
3
replies
264
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 5 days ago by
Ram
44k • written 5 days ago by
sooni
▴ 20
0
votes
5
replies
348
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
1
vote
1
reply
256
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
6 days ago by
ramiro.barrantes
• 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 6 days ago by
Ram
44k • written 3.9 years ago by
millere
• 0
0
votes
1
reply
183
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 5 days ago by
Michael
54k • written 6 days ago by
mgranada3
▴ 30
0
votes
1
reply
167
views
Add line under stat test
stats
R
updated 4 days ago by
Nyksubuz
▴ 20 • written 6 days ago by
Ghada
• 0
1
vote
5
replies
814
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
117
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Rodolfo Adrián
• 0
1
vote
4
replies
250
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
2 hours ago by
shpak.max
▴ 50
2
votes
4
replies
291
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 6 days ago by
yura.grabovska
▴ 90 • written 6 days ago by
ev97
▴ 20
1
vote
16
replies
789
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 3 days ago by
GenoMax
142k • written 6 days ago by
hophuquy0944
• 0
0
votes
4
replies
260
views
Sequencing Depth (Read Depth) Calculations
depth
5 days ago by
LucisTheFather
• 0
0
votes
1
reply
145
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
6 days ago by
asalimih
▴ 60
0
votes
0
replies
116
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
6 days ago by
jway
• 0
2
votes
2
replies
202
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 5 days ago by
Ram
44k • written 6 days ago by
jsmith120f
• 0
2
votes
2
replies
213
views
genome finishing
finishing
genome
updated 6 days ago by
nd48
▴ 30 • written 6 days ago by
trezini
• 0
1
vote
5
replies
243
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 6 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
biology_inform
▴ 50
1
vote
4
replies
313
views
Add stats to boxplot in R
stats
R
6 days ago by
Ghada
• 0
0
votes
1
reply
166
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 5 days ago by
Papyrus
★ 2.9k • written 6 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
161
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 5 days ago by
GenoMax
142k • written 6 days ago by
Lélé
▴ 10
0
votes
5
replies
321
views
calculating genomic coverage/ base overlap in R
genomics
updated 3 days ago by
1769mkc
★ 1.2k • written 6 days ago by
Xbox_27
• 0
1
vote
5
replies
288
views
Annotating file using bcftools
annotation
plink
bcftools
5 days ago by
kl
▴ 10
0
votes
9
replies
390
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
5 days ago by
njornet
▴ 20
0
votes
3
replies
185
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
6 days ago by
Esraa
• 0
3
votes
3
replies
249
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 5 days ago by
ATpoint
82k • written 6 days ago by
Alexandra
• 0
4
votes
1
reply
341
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 6 days ago by
dariober
14k • written 7 days ago by
Holly
▴ 30
1
vote
4
replies
304
views
Filtering VCF files based on VAF giving incorrect results
GATK
picard
VCF
bcftools
updated 4 hours ago by
Ram
44k • written 6 days ago by
Arton
▴ 10
0
votes
0
replies
101
views
ReactomeGSA
ReactomeGSA
6 days ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
90
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
6 days ago by
Transmitting Science communication
▴ 70
0
votes
5
replies
303
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 5 days ago by
GenoMax
142k • written 6 days ago by
chrisk
• 0
711 results • Page
3 of 15
Recent Votes
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
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
Answer: Functional enrichment analysis for unique gene IDs
Comment: Super ehancers
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Recent Replies
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 …
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
I want to get lot of files through code
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