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181 results • Page
2 of 4
Sort: Views
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Views
Votes
Replies
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
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
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
0
votes
4
replies
332
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
2 days ago by
Bibi
• 0
2
votes
3
replies
330
views
Trimming tool
Trimming
updated 1 day ago by
Ram
44k • written 4 days ago by
GeneC
• 0
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
0
votes
2
replies
319
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
2 days ago by
Ezequiel
• 0
2
votes
4
replies
314
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
6 days ago by
Esraa
• 0
1
vote
4
replies
313
views
Add stats to boxplot in R
stats
R
6 days ago by
Ghada
• 0
1
vote
3
replies
304
views
Using ggplotly in R
ggplot
ggplotly
updated 6 days ago by
jared.andrews07
★ 17k • written 7 days ago by
jen
▴ 10
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
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
0
votes
2
replies
303
views
Traveler with Infernal mapping failed
r2dt
updated 3 days ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 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
1
vote
3
replies
294
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 5 days ago by
GenoMax
142k • written 7 days ago by
ohtang7
▴ 40
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
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
2
votes
2
replies
291
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 5 days ago by
Ram
44k • written 5 days ago by
txema.heredia
▴ 130
1
vote
5
replies
288
views
Annotating file using bcftools
annotation
plink
bcftools
5 days ago by
kl
▴ 10
1
vote
4
replies
268
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 1 day ago by
Ram
44k • written 1 day ago by
Harshita
• 0
0
votes
2
replies
268
views
How can I calculate the OS of each patient?
overall-survival
1 day ago by
Pedro
• 0
0
votes
2
replies
268
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 4 days ago by
LauferVA
4.2k • written 4 days ago by
ijarne
• 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
4
replies
260
views
Sequencing Depth (Read Depth) Calculations
depth
5 days ago by
LucisTheFather
• 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
2
replies
258
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
melissachua90
▴ 70
2
votes
1
reply
257
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 3 days ago by
Gordon Smyth
★ 7.2k • written 4 days ago by
marineandriot
• 0
1
vote
1
reply
256
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
6 days ago by
ramiro.barrantes
• 0
1
vote
4
replies
250
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
2 hours ago by
shpak.max
▴ 50
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
2
votes
2
replies
249
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
5 days ago by
bioinfo
▴ 150
0
votes
4
replies
246
views
GO analysis: p-value range
GO
R
updated 1 day ago by
Matthias Zepper
4.6k • written 1 day ago by
sooni
▴ 20
1
vote
2
replies
245
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
6 days ago by
MarcosCosta
• 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
0
votes
3
replies
237
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 1 day ago by
GenoMax
142k • written 2 days ago by
KHURRAM SHAHZAD
• 0
0
votes
2
replies
235
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
6 days ago by
Chen
• 0
1
vote
2
replies
227
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 15 hours ago by
colindaven
6.4k • written 2 days ago by
Dr.
• 0
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
0
votes
3
replies
225
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 1 day ago by
marco.barr
▴ 130 • written 1 day ago by
Mohamed Samir
▴ 20
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
5
replies
224
views
Why most genes have high padj values
RNA-seq
DEG
updated 1 day ago by
Ram
44k • written 1 day ago by
mnx0723
• 0
1
vote
2
replies
220
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 6 days ago by
colindaven
6.4k • written 6 days ago by
mbrav005
• 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
2
votes
4
replies
212
views
Filter Genome for Specific Sites
bedtools
updated 1 day ago by
Ram
44k • written 1 day ago by
Anita
• 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
2
replies
210
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
6 days ago by
melissa.joubert
• 0
1
vote
1
reply
207
views
constructing pangenome through psvcp
psvcp
pangenome
3 days ago by
analyst
▴ 50
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
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
1
vote
2
replies
196
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 7 hours ago by
geneontologyhelp
▴ 410 • written 1 day ago by
Pegasus
▴ 100
181 results • Page
2 of 4
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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