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116,586 results • Page
1 of 2332
Sort: Rank
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Votes
Replies
0
votes
4
replies
501
views
Adding CB tag to bam file
samtools
bam
25 minutes ago by
Maria
• 0
1
vote
8
replies
724
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
updated 34 minutes ago by
haibol2017
▴ 10 • written 3 months ago by
DKA
▴ 40
0
votes
0
replies
15
views
Finding orthologs between genome error
OMA
OMAbrowser
47 minutes ago by
hemantcnaik
• 0
0
votes
2
replies
691
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 1 hour ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
3
replies
101
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 2 hours ago by
GenoMax
141k • written 4 hours ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
42
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
how-to
2 hours ago by
glaciya2018
• 0
0
votes
0
replies
33
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
variantcalling
DNAseq
illumina
RNAseq
transcriptomics
4 hours ago by
David Langenberger
11k
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
42
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
4 hours ago by
pramach1
▴ 40
0
votes
14
replies
3.4k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 5 hours ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
1
reply
65
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 2 hours ago by
Sofia
• 0 • written 6 hours ago by
mawigoj318
• 0
0
votes
0
replies
62
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
8 hours ago by
salias
• 0
4
votes
5
replies
223
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 1 hour ago by
swbarnes2
14k • written 12 hours ago by
VITALA
• 0
0
votes
2
replies
119
views
different FeatureCounts output for the same data
fpkm
rnaseq
Counts
Rsubread
updated 5 hours ago by
Istvan Albert
100k • written 9 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
50
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
single-cell
suppa
rnaseq
splicing
alternative
3 hours ago by
newuser2024
• 0
0
votes
0
replies
44
views
Network Alignment
plugin
Cytoscape
CytoMCS
9 hours ago by
Akash D
▴ 40
0
votes
1
reply
92
views
alignment result
RNA-seq
samtool
analysis
hisat2
updated 6 hours ago by
GenoMax
141k • written 10 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
49
views
News:
hands-on introduction to generalized linear models (GLMs) using R
GeneralizedLinearModels
GLMs
R
11 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
48
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
hetero
Seurat
modelHomotypic
DoubletFinder
11 hours ago by
Jeyong
• 0
0
votes
2
replies
121
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 1 hour ago by
swbarnes2
14k • written 13 hours ago by
Aaliya
• 0
0
votes
2
replies
158
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
5 hours ago by
mropri
▴ 150
2
votes
2
replies
140
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 13 hours ago by
analyst
▴ 30 • written 18 hours ago by
lorena9132
• 0
0
votes
0
replies
64
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
18 hours ago by
Kash
▴ 110
7
votes
2
replies
204
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 19 hours ago by
geneontologyhelp
▴ 390 • written 2 days ago by
catherine.teyssier
• 0
0
votes
1
reply
153
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 19 hours ago by
Istvan Albert
100k • written 2 days ago by
Abeer
• 0
0
votes
4
replies
232
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 19 hours ago by
swbarnes2
14k • written 1 day ago by
dxj294
• 0
0
votes
1
reply
103
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 14 hours ago by
Mensur Dlakic
★ 27k • written 20 hours ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
182
views
How to calculate identity percentage between proteins contained in a FASTA file?
percentage
FASTA
alignment
identity
updated 9 hours ago by
b.contreras.moreira
▴ 170 • written 20 hours ago by
v.berriosfarias
▴ 140
2
votes
1
reply
157
views
Seurat merge and batch correction
Seurat
updated 21 hours ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
1
vote
1
reply
128
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated 21 hours ago by
Pierre Lindenbaum
161k • written 21 hours ago by
Biostar
2.7k
1
vote
1
reply
106
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 22 hours ago by
GenoMax
141k • written 22 hours ago by
heelpPlease
• 0
2
votes
9
replies
774
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 17 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
10
replies
338
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
14 hours ago by
atowns21
• 0
0
votes
1
reply
115
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 22 hours ago by
bk11
★ 2.3k • written 23 hours ago by
alphaflylizard
• 0
3
votes
3
replies
174
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 23 hours ago by
GenoMax
141k • written 1 day ago by
Estevão
• 0
0
votes
3
replies
195
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 20 hours ago by
Istvan Albert
100k • written 1 day ago by
Dylan
• 0
1
vote
4
replies
152
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 50 minutes ago by
GenoMax
141k • written 1 day ago by
Lada
▴ 30
4
votes
11
replies
453
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 17 hours ago by
LauferVA
4.2k • written 1 day ago by
dominickd
• 0
3
votes
13
replies
562
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 1 hour ago by
bk11
★ 2.3k • written 6 weeks ago by
Sofia
• 0
0
votes
0
replies
73
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
1 day ago by
ohtang7
▴ 40
3
votes
0
replies
93
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
2
votes
2
replies
390
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 1 day ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
0
votes
1
reply
129
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Srinka
▴ 20
8
votes
5
replies
4.9k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
0
votes
5
replies
252
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
7 hours ago by
njornet
▴ 20
5
votes
4
replies
602
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
12 hours ago by
kirillkirilenko
▴ 40
0
votes
0
replies
75
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 1 day ago by
Ram
43k • written 1 day ago by
SHREYA
• 0
0
votes
3
replies
352
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 1 day ago by
colindaven
6.4k • written 9 days ago by
rj.rezwan
• 0
0
votes
0
replies
87
views
Merging replicates from Encode project
CHIP-seq
encode
1 day ago by
Nurken
• 0
1
vote
3
replies
187
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
116,586 results • Page
1 of 2332
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Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
A: Where To Download Pam50 Gene Set?
Answer: Fail to install umap-learn in R
Answer: Fail to install umap-learn in R
Answer: Fail to install umap-learn in R
What are Tiles in Sequencing
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Recent Replies
Answer: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
GenoMax
141k
`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Cross posted here (including the code used to make up the counts): https://support.bioconductor.org/p/9157911/#9157959
Comment: To get p-values for the TPM
by
swbarnes2
14k
RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
i checked both of these programs (`bbduk` and `fastp`) and it seems they use reads as inputs (fastq formats)... how can I trim my transcrip…
Comment: AGeNT LocatIt
by
barslmn
★ 2.1k
He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
This looks good. Please try with using `--allow-no-sex flag` plink --bfile your_data_phenoUP --assoc --allow-no-sex --out your_data_ph…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
SC899359_PC75420_A05 SC899359_PC75420_A05 0 0 0 2 SC899360_PC75415_D01 SC899360_PC75415_D01 0 0 0 2 SC899361_PC75425_H05 SC899361_PC75425_H…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Please show me a few lines of phenotype updated .fam file. You can do `head your_data_phenoUP.fam` and paste result here. Please do not us…
Comment: GEMMA GWAS how to specify factor or numerical for covariates
by
Sofia
• 0
Hi, I don't have a solution to your question but I followed this tutorial and was helpful to me in my analysis https://youtu.be/NusV6duyvXs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
Catalog file lists the genomes included. There seem to be 71365 unique items in field 2. 2 Bacteria WP_000018326.1 4459…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
yes sure ! ![enter image description here][1] [1]: /media/images/f0f94f6c-4387-4188-a1aa-19152a89
Answer: AGeNT LocatIt
by
Greg
• 0
Give it more memory. ~10x more memory, or whatever you can give it, I had samples that weren't even close to being done after 3.5 da…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Thanks! I've already tried looking through these files, I need release 83. I am trying to find this information in the .catalog file of the…
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