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1,000 results • Page
6 of 20
Sort: Votes
Rank
Views
Votes
Replies
3
votes
5
replies
707
views
Salmon loop on multiple samples
Salmon
updated 7 months ago by
Ram
44k • written 7 months ago by
m.storti
• 0
3
votes
6
replies
883
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 5 months ago by
jv
★ 1.8k • written 5 months ago by
newbee
▴ 40
3
votes
8
replies
2.0k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 12 months ago by
Ram
44k • written 5.6 years ago by
nagendranp1991
• 0
3
votes
5
replies
1.3k
views
Running purge_dups on a hybrid assembly (optical mapping + reads)
pacbio
purge_dups
Assembly
bionano
updated 8 months ago by
colindaven
6.4k • written 3.3 years ago by
pablo
▴ 300
3
votes
3
replies
887
views
from fasta to gtf format?
gtf
DE
fasta
updated 4 months ago by
e.r.zakiev
▴ 210 • written 3.1 years ago by
debitboro
▴ 260
3
votes
2
replies
753
views
Scvelo vs Monocle3
monocle3
scvelo
7 months ago by
Chris
▴ 280
3
votes
14
replies
6.1k
views
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn
mbedtls
blast
linux
blast+
updated 4 months ago by
K.Gee
▴ 40 • written 3.2 years ago by
janneken0210
• 0
3
votes
10
replies
1.3k
views
STAR index not working
STAR
RNA-Seq
8 months ago by
camillab.
▴ 160
3
votes
3
replies
355
views
learning bioinformatics
course
learning
updated 4 months ago by
Ram
44k • written 4 months ago by
sevda
• 0
3
votes
9
replies
1.7k
views
How to get negative training set if I don't know what constitutes negative?
machine-learning
dna-sequence
blast
updated 6 months ago by
Ram
44k • written 7.7 years ago by
nafizh
• 0
3
votes
6
replies
839
views
Annotating genome based on Sequence
genome
annotation
updated 6 months ago by
Darked89
4.6k • written 6 months ago by
buhbs
▴ 30
3
votes
3
replies
1.1k
views
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
scRNA-seq
RNA-Seq
Seurat
updated 7 months ago by
bk11
★ 2.5k • written 7 months ago by
prietto
▴ 10
3
votes
2
replies
306
views
Inject haplotypes into rGFA?
Pangenome
3 months ago by
agd27
▴ 130
3
votes
2
replies
1.3k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 4 weeks ago by
Ram
44k • written 4.5 years ago by
baldissera152
▴ 10
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length
Bed
updated 11 months ago by
Ram
44k • written 4.3 years ago by
Ankit
▴ 500
3
votes
3
replies
473
views
I can't add VAF from population for all of my variants from VCF file
genomics
vcf
gnomad
updated 10 weeks ago by
Ram
44k • written 10 weeks ago by
Samuel
▴ 20
3
votes
6
replies
2.5k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 5 weeks ago by
Ram
44k • written 22 months ago by
ev97
▴ 20
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 11 months ago by
Ram
44k • written 5.2 years ago by
Star
▴ 60
3
votes
5
replies
3.2k
views
GO annotation for rice in an R package
annotation
R
updated 3 months ago by
prity6459
• 0 • written 7.5 years ago by
djyjin
▴ 10
3
votes
4
replies
372
views
What should be used as a "baseline" in pooled CRISPR screen?
CRISPR
MAGECK
FACS
10 weeks ago by
Aleksandr
▴ 10
3
votes
5
replies
1.6k
views
Uniprot API access to download .pdb files
PDB
API
Python
Uniprot
12 months ago by
BioGrad321
• 0
3
votes
4
replies
847
views
Downstream analysis with DEseq2 normalization
DEseq2
integration
6 months ago by
QX
• 0
3
votes
1
reply
595
views
PLINK .ped file issue
plink
updated 7 months ago by
Ram
44k • written 7 months ago by
plinknoob23
• 0
2
votes
1
reply
972
views
How to evaluate the performance of an RNA-seq pipeline
Differential-gene-expression
RNA-Seq
R
DESeq2
updated 6 weeks ago by
Ram
44k • written 4.1 years ago by
nhaus
▴ 360
2
votes
5
replies
3.3k
views
How to output colored alignment from clustal omega stand alone tool?
Clustal Omega
Colored alignment
updated 9 months ago by
Joe
21k • written 4.8 years ago by
MB
▴ 50
2
votes
3
replies
803
views
Ion torrent
ion
torrent
11 months ago by
alexandra
• 0
2
votes
3
replies
761
views
single exon quantification using RNA-seq
mRNA
RNA-seq
11 months ago by
Qianjiang(QJ) Hu
▴ 10
2
votes
2
replies
352
views
Extracting mutation information from a VCF file.
Biopython
VCF
phylogenetic
UShER
updated 3 months ago by
Pierre Lindenbaum
161k • written 3 months ago by
realtreeecat
• 0
2
votes
5
replies
1.1k
views
PlotHeatmap in deeptools horizontally
plotHeatmap
cutrun
chip-seq
deeptools
updated 11 months ago by
Ram
44k • written 22 months ago by
minoo
▴ 10
2
votes
2
replies
1.4k
views
tool or software to design graphical images for given fusion gene data?
fusion-gene
updated 10 months ago by
Ram
44k • written 8.9 years ago by
gskbioinfo143
▴ 60
2
votes
13
replies
2.2k
views
RepeatMasker error when trying to generate repeat sequence distribution pie chart (all code and errors provided)
repeatmasker
updated 7 months ago by
Ram
44k • written 9 months ago by
epianalysis
• 0
2
votes
4
replies
1.1k
views
Sort BAM file by read mates
samtools
alignment
sequencing
updated 11 months ago by
Ram
44k • written 18 months ago by
StringTheory
• 0
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression
RNA-Seq
DESeq2
updated 6 weeks ago by
Ram
44k • written 8.1 years ago by
Chris Gene
▴ 80
2
votes
5
replies
917
views
ATAC-seq troubleshoot - Just Noise
ATAC-seq
updated 7 months ago by
ATpoint
82k • written 8 months ago by
vk
▴ 40
2
votes
4
replies
758
views
Prediction of novel variants
annovar
updated 11 months ago by
Ram
44k • written 3.7 years ago by
syedahamdani94
• 0
2
votes
2
replies
653
views
Bio.Phylo cut the tree (python)
phylogeny
cuttree
biopython
tree
Bio.Phylo
9 months ago by
Fedor
▴ 10
2
votes
4
replies
827
views
fasttree running problem
fasttree
9 months ago by
chopinone
• 0
2
votes
2
replies
631
views
chromosomal distribution with sequence data
gene
genome
alignment
sequence
updated 11 months ago by
Ram
44k • written 4.3 years ago by
shwetamgr1
▴ 10
2
votes
2
replies
742
views
Pangenome using Orthofinder
OrthoFinder
Pangenome
bacteria
8 months ago by
kirankumareripogu
▴ 10
2
votes
8
replies
745
views
TCGA Biospecimens Slides Extraction
tcga
updated 12 weeks ago by
Zhenyu Zhang
★ 1.2k • written 3 months ago by
jain72744
▴ 10
2
votes
3
replies
2.0k
views
SnpEff html and .vcf file result are not matching
vcf
SNP
snpeff
updated 11 months ago by
Ram
44k • written 6.8 years ago by
misbahabas
▴ 70
2
votes
2
replies
509
views
How to find the Allele Number (AN) of a variant not reported on gnomAD
gnomad
variant
updated 6 months ago by
Jeremy Leipzig
22k • written 6 months ago by
Lisa392
• 0
2
votes
4
replies
975
views
Specific case of "bedtools intersect"
bedtools
BAM
updated 11 months ago by
Ram
44k • written 2.1 years ago by
predeus
★ 2.0k
2
votes
1
reply
511
views
Filtering content in heatmap to highest values
R
heatmap
ggplot2
11 months ago by
cthangav
▴ 100
2
votes
6
replies
677
views
Match variants from RNAseq with known databases
dbsnp
SNP
vcf
bcftools
RNA-seq
7 months ago by
dilokef367
• 0
2
votes
2
replies
290
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 7 weeks ago by
Pierre Lindenbaum
161k • written 8 weeks ago by
fred.s.kremer
▴ 110
2
votes
2
replies
1.1k
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 5 months ago by
cmdcolin
★ 3.8k • written 5 months ago by
Dylan C-C
• 0
2
votes
4
replies
633
views
Refseq annotation | Populus trichocarpa
R
RNA-seq
plants
Refseq
updated 8 months ago by
Ram
44k • written 8 months ago by
P
• 0
2
votes
4
replies
979
views
Downloading all the heteroComplex protein PDB IDs in RCSB Protein Data Bank
python
biopython
updated 11 months ago by
Ram
44k • written 4.6 years ago by
Christian
• 0
2
votes
1
reply
294
views
Conversion Issue with bcl2fastq2
bcl2fastq2
Novaseq6000
updated 3 months ago by
Ram
44k • written 3 months ago by
Christopher
• 0
1,000 results • Page
6 of 20
Recent Votes
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T2T-CHM13 "complete" human genome gff/gtf annotation file
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
Yes please see below: TraesCS2B02G372900 TraesCS2B02G375100 TraesCS2B02G374700 TraesCS2B02G382000
Comment: Functional enrichment analysis for unique gene IDs
by
Pegasus
▴ 100
Thanks for your answer, but as far as I know, gProfiler2 does not support bacteria. Could you please suggest alternative websites or softwa…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Hi Alex, I'm sorry if I wasn't initially clear! The question hasn't changed; I had written in this post that I wanted all pairwise combinat…
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
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Ghada
• 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
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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…
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