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116,563 results • Page
1 of 2332
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0
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0
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Which software tool do Bioinformaticians generally use for secondary structure assignment?
secondary-structure
protein
just now by
4fzcgueyp5
• 0
0
votes
0
replies
18
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
28 minutes ago by
Dylan
• 0
0
votes
1
reply
18
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 16 minutes ago by
GenoMax
141k • written 34 minutes ago by
Lada
▴ 30
3
votes
11
replies
273
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated just now by
GenoMax
141k • written 16 hours ago by
dominickd
• 0
3
votes
6
replies
268
views
How to convert plink files to Hapmap Format
GWAS
Plink
just now by
Sofia
• 0
0
votes
0
replies
13
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
1 hour ago by
ohtang7
▴ 40
0
votes
0
replies
20
views
How to merge UMAP coordinates with the concatenated loom files in anndata object
RNA-velocity
scanpy
loomfile
scvelo
python
1 hour ago by
Kash
▴ 110
2
votes
0
replies
37
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 2 hours ago by
Ram
43k • written 2 hours ago by
carlopecoraro2
★ 2.5k
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
2
votes
2
replies
331
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 3 hours ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
0
votes
1
reply
65
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 4 hours ago by
GenoMax
141k • written 4 hours ago by
Srinka
▴ 20
7
votes
5
replies
4.6k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 50
0
votes
4
replies
129
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
updated 2 hours ago by
GenoMax
141k • written 4 hours ago by
njornet
▴ 20
5
votes
3
replies
514
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 5 hours ago by
colindaven
6.4k • written 5 days ago by
kirillkirilenko
▴ 40
0
votes
0
replies
34
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 2 hours ago by
Ram
43k • written 5 hours ago by
SHREYA
• 0
0
votes
3
replies
306
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 5 hours ago by
colindaven
6.4k • written 8 days ago by
rj.rezwan
• 0
0
votes
0
replies
39
views
Merging replicates from Encode project
CHIP-seq
encode
5 hours ago by
Nurken
• 0
1
vote
3
replies
135
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
6 hours ago by
WouterDeCoster
47k
0
votes
3
replies
134
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 4 hours ago by
mchour
• 0 • written 7 hours ago by
rhossen
• 0
0
votes
1
reply
95
views
WGCNA preservation analysis
WGCNA
preservation
updated 7 hours ago by
Michael
54k • written 8 hours ago by
michael.flower.14
▴ 180
0
votes
2
replies
106
views
some error in building kraken2 database
metagenome
kraken2
updated 2 hours ago by
Ram
43k • written 7 hours ago by
Art1ess
• 0
0
votes
1
reply
57
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 2 hours ago by
bk11
★ 2.3k • written 8 hours ago by
Susmita Mandal
▴ 110
0
votes
1
reply
78
views
Plots for DNA methylation data
plots
DNA
methylation
updated 5 hours ago by
GenoMax
141k • written 9 hours ago by
sarahawan92
▴ 10
0
votes
3
replies
438
views
python file for coding potential calculator
cpc2.py
updated 9 hours ago by
atharvakarkare14
▴ 10 • written 4 days ago by
Ashok
• 0
1
vote
1
reply
105
views
Failed kmer content
kmer
illumina
ngs
updated 2 hours ago by
Ram
43k • written 10 hours ago by
Kasturi
• 0
0
votes
1
reply
101
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 9 hours ago by
Basti
★ 2.0k • written 11 hours ago by
qudrat.nii
▴ 10
0
votes
0
replies
75
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
12 hours ago by
yxwucq
• 0
0
votes
0
replies
58
views
Seurat merge and batch correction
Seurat
13 hours ago by
sooni
▴ 20
0
votes
0
replies
44
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 1 hour ago by
Ram
43k • written 13 hours ago by
SSSJec
• 0
0
votes
5
replies
203
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
updated 17 hours ago by
Pierre Lindenbaum
161k • written 20 hours ago by
Sd
• 0
0
votes
2
replies
133
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
20 hours ago by
sainavyav22
• 0
0
votes
1
reply
101
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 21 hours ago by
Ram
43k • written 21 hours ago by
Cameron.walker9900
• 0
0
votes
8
replies
233
views
Error in cnetplot enrichplot package
R
updated 20 hours ago by
Ram
43k • written 22 hours ago by
Farhad
• 0
1
vote
4
replies
166
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 22 hours ago by
Mensur Dlakic
★ 27k • written 22 hours ago by
Κοσμάς
• 0
0
votes
0
replies
76
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 22 hours ago by
Ram
43k • written 22 hours ago by
maxime.policarpo
▴ 200
3
votes
3
replies
140
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 22 hours ago by
Mensur Dlakic
★ 27k • written 22 hours ago by
c_u
▴ 520
0
votes
0
replies
63
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 22 hours ago by
Ram
43k • written 22 hours ago by
sansan_96
▴ 80
0
votes
2
replies
121
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
21 hours ago by
dxj294
• 0
0
votes
0
replies
68
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 2 hours ago by
Ram
43k • written 22 hours ago by
Amélie
• 0
0
votes
0
replies
105
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 22 hours ago by
Ram
43k • written 23 hours ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 20 hours ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
2
votes
1
reply
111
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
ATpoint
81k • written 1 day ago by
catherine.teyssier
• 0
2
votes
3
replies
159
views
from row count to tpm
tpm
row-count
normalization
9 hours ago by
michelafrancesconi9
▴ 20
0
votes
0
replies
71
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Abeer
• 0
1
vote
4
replies
169
views
Downsampling fastq file
downsample
fastq
updated 1 day ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 80
2
votes
3
replies
297
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 1 day ago by
dsull
★ 5.8k • written 14 days ago by
javanokendo
▴ 60
0
votes
1
reply
111
views
tbtool
tbtool
updated 1 day ago by
Ram
43k • written 1 day ago by
Raman
• 0
0
votes
2
replies
163
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 23 hours ago by
i.sudbery
19k • written 1 day ago by
Patadu94
• 0
3
votes
3
replies
185
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Mariana
▴ 10
0
votes
2
replies
136
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 22 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
emmanouil.a
▴ 120
116,563 results • Page
1 of 2332
Recent Votes
Comment: How to convert plink files to Hapmap Format
Am I crazy, or are most published RNA-seq studies vastly underpowered?
Trimming sequences based on NCBI contamination screen report
warning[vg::giraffe]: Cannot cluster reads with a fragment distance smaller than read distance
Answer: Redirection of Duplicate PMIDs
Answer: How to convert plink files to Hapmap Format
Answer: How to convert plink files to Hapmap Format
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★ 2.4k
Scholar
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marco.barr
▴ 80
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Recent Replies
Comment: Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Ser
by
atowns21
• 0
@benjamin.pyenson and @Ram could you share an example command of using STARSolo for the alignment? Did you use the json file directly? Or d…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
GenoMax
141k
> I didn't do a good job with Trimmomatic for some reason so I have to do some trimming of my transcripts. If you had extraneous sequence…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Please answer my above question. What type of data is it, binary (cases and controls) or quantitative? You need to update Phenotype info in…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
This is how my .fam file looks like ![enter image description here][1] [1]: /media/images/caccd97c-3606-48d2-aa32-423a9882 And I run …
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
What type of phenotype is in your data? It looks like it does not have affection status (default values for affection status will be: 1 = u…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Agree. This is also a great solution that flips the problem on its head, as it were, Dominick. I dont want to be preachy, but this is why i…
Answer: Redirection of Duplicate PMIDs
by
GenoMax
141k
> linked to a list of grants Using [**EntrezDirect**][1] this may be much simpler if you have the grant number available. I tested this w…
Answer: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Hi Dominick, One thing I am not sure of is, how is it that you got the other PMID in the first place? The reason I ask is that you mentio…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thanks Marco, btw do you have any idea why I get this "Warning: Skipping --assoc/--model since less than two phenotypes are present." aft…
Comment: Subset Seurat object from Xenium spatial data
by
bk11
★ 2.3k
For subsetting a sample, you can do something like this- Idents(seuratObj) <- "orig.ident" subj1 <- c("subject_1") subj1_seur…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Ok! I have a recommendation. I'll submit it as an answer, pending your feedback. vincent
Comment: DYH17 Structure Prediction
by
anasjamshed
▴ 120
In modeller we need to use templates as well.so 63% is acceptable
Comment: DYH17 Structure Prediction
by
Ram
43k
Mensur said > The latter option assumes you know how to use Modeller Do you know how to use Modeller? I vaguely recall there being a mini…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
GenoMax
141k
OP is working with long reads so the chances of reads aligning to unlocalized scaffolds are relatively small. Doing some testing may be suf…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
ATpoint
81k
I personally think that comparing the same peak between conditions is meaningful and comparing peaks within the same sample is not.
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