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181 results • Page
2 of 4
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Votes
Replies
2
votes
4
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212
views
Filter Genome for Specific Sites
bedtools
updated 1 day ago by
Ram
44k • written 1 day ago by
Anita
• 0
1
vote
4
replies
270
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
4
replies
109
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
2 hours ago by
shpak.max
▴ 50
0
votes
4
replies
246
views
GO analysis: p-value range
GO
R
updated 1 day ago by
Matthias Zepper
4.6k • written 2 days ago by
sooni
▴ 20
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
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
1
vote
4
replies
348
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 3 days ago by
Joe
21k • written 13 days ago by
cput
• 0
0
votes
4
replies
367
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 3 days ago by
txema.heredia
▴ 130 • written 5 days ago by
Ngrin
• 0
1
vote
4
replies
255
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
3 hours ago by
shpak.max
▴ 50
0
votes
3
replies
232
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 21 minutes ago by
Nyksubuz
▴ 20 • written 5 days ago by
Luqman
• 0
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
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
3
votes
3
replies
250
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
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
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 8 days ago by
ohtang7
▴ 40
1
vote
3
replies
811
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 5 days ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
1
vote
3
replies
302
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
2
votes
3
replies
265
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
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
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
3
replies
189
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 1 day ago by
Ram
44k • written 1 day ago by
Bioinformatics_begginner
▴ 20
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
3
replies
226
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
3
replies
525
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 13 hours ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
2
votes
3
replies
1.1k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
updated 6 hours ago by
finch
• 0 • written 19 months ago by
Aspire
▴ 330
0
votes
3
replies
117
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 5 hours ago by
Ram
44k • written 11 hours ago by
pirku
• 0
0
votes
3
replies
1.7k
views
Running STRUCTURE from command line
STRUCTURE
updated 5 hours ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
0
votes
3
replies
109
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 4 hours ago by
GenoMax
142k • written 4 hours ago by
bioinfo
▴ 150
1
vote
3
replies
130
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 4 hours ago by
Pierre Lindenbaum
161k • written 8 hours ago by
mrk
• 0
1
vote
2
replies
126
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 6 hours ago by
Ram
44k • written 9 hours ago by
Harshita
• 0
0
votes
2
replies
259
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
2
replies
250
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
1
vote
2
replies
176
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
1 day ago by
ojaswinipandey
• 0
0
votes
2
replies
130
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
7 hours ago by
Shukai
• 0
0
votes
2
replies
103
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
updated 3 hours ago by
LChart
3.9k • written 6 hours ago by
Arton
▴ 10
0
votes
2
replies
80
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
1
vote
2
replies
201
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 7 hours ago by
geneontologyhelp
▴ 410 • written 1 day ago by
Pegasus
▴ 100
0
votes
2
replies
131
views
z-score of gene set
z-score
scRNA
gene-set
updated 8 hours ago by
Ram
44k • written 10 hours ago by
Hien
• 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 7 days ago by
mbrav005
• 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
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
0
votes
2
replies
268
views
How can I calculate the OS of each patient?
overall-survival
1 day ago by
Pedro
• 0
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
0
votes
2
replies
191
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
1 day ago by
sainavyav22
• 0
1
vote
2
replies
175
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 1 day ago by
Ram
44k • written 1 day ago by
Sony
▴ 10
1
vote
2
replies
724
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 2 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 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
0
votes
2
replies
172
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
10 hours ago by
Bjorn
• 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
0
votes
2
replies
270
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 4 days ago by
LauferVA
4.2k • written 4 days ago by
ijarne
• 0
181 results • Page
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Comment: Problem in getting geo file through GEOQUERY
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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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