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116,558 results • Page
1 of 2332
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News:
Online Cours on Spatial Omics in R/Bioconductor (last 4 seats available)
SpatialTranscriptomics
Bioconductor
SpatialOmics
3 minutes ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
284
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 46 minutes ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 70
0
votes
1
reply
25
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 1 hour ago by
GenoMax
141k • written 1 hour ago by
Srinka
▴ 20
7
votes
5
replies
4.5k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 50
0
votes
3
replies
37
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
updated 4 minutes ago by
ATpoint
81k • written 2 hours ago by
njornet
▴ 20
5
votes
3
replies
488
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 2 hours ago by
colindaven
6.4k • written 5 days ago by
kirillkirilenko
▴ 40
0
votes
0
replies
18
views
Software to calculate RSCU, ENC other than codonw
rscu
bioinformatics
codonw
2 hours ago by
SHREYA
• 0
0
votes
3
replies
282
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 2 hours ago by
colindaven
6.4k • written 8 days ago by
rj.rezwan
• 0
0
votes
0
replies
24
views
Merging replicates from Encode project
CHIP-seq
encode
3 hours ago by
Nurken
• 0
1
vote
3
replies
121
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
4 hours ago by
WouterDeCoster
47k
0
votes
3
replies
94
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 1 hour ago by
mchour
• 0 • written 4 hours ago by
rhossen
• 0
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
1
reply
80
views
WGCNA preservation analysis
WGCNA
preservation
updated 4 hours ago by
Michael
54k • written 6 hours ago by
michael.flower.14
▴ 180
0
votes
2
replies
79
views
some error in building kraken2 database
metagenome
database
bioinformatics
kraken2
updated 2 hours ago by
GenoMax
141k • written 4 hours ago by
Art1ess
• 0
0
votes
0
replies
29
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
5 hours ago by
Susmita Mandal
▴ 110
0
votes
1
reply
72
views
Plots for DNA methylation data
plots
DNA
methylation
updated 3 hours ago by
GenoMax
141k • written 6 hours ago by
sarahawan92
▴ 10
0
votes
3
replies
428
views
python file for coding potential calculator
cpc2.py
updated 6 hours ago by
atharvakarkare14
▴ 10 • written 4 days ago by
Ashok
• 0
0
votes
1
reply
73
views
Failed kmer content
content
kmer
illumina
ngs
updated 3 hours ago by
GenoMax
141k • written 7 hours ago by
Kasturi
• 0
0
votes
1
reply
92
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 6 hours ago by
Basti
★ 2.0k • written 9 hours ago by
qudrat.nii
▴ 10
0
votes
0
replies
69
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
10 hours ago by
yxwucq
• 0
0
votes
0
replies
52
views
Seurat merge and batch correction
Seurat
10 hours ago by
sooni
▴ 20
0
votes
0
replies
38
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
R
Copy-number-analysis
gc.wig
genome
10 hours ago by
SSSJec
• 0
1
vote
6
replies
178
views
Redirection of Duplicate PMIDs
error
pmid
how-to
53 minutes ago by
dominickd
• 0
0
votes
5
replies
199
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
updated 15 hours ago by
Pierre Lindenbaum
161k • written 18 hours ago by
Sd
• 0
0
votes
2
replies
128
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
17 hours ago by
sainavyav22
• 0
0
votes
1
reply
96
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 18 hours ago by
Ram
43k • written 19 hours ago by
Cameron.walker9900
• 0
0
votes
8
replies
228
views
Error in cnetplot enrichplot package
R
updated 17 hours ago by
Ram
43k • written 19 hours ago by
Farhad
• 0
1
vote
4
replies
161
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 19 hours ago by
Mensur Dlakic
★ 27k • written 19 hours ago by
Κοσμάς
• 0
0
votes
0
replies
71
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 19 hours ago by
Ram
43k • written 19 hours ago by
maxime.policarpo
▴ 200
3
votes
3
replies
135
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 19 hours ago by
Mensur Dlakic
★ 27k • written 19 hours ago by
c_u
▴ 520
0
votes
0
replies
59
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 19 hours ago by
Ram
43k • written 20 hours ago by
sansan_96
▴ 80
0
votes
2
replies
116
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
18 hours ago by
dxj294
• 0
0
votes
0
replies
61
views
File with NCBI summary or Uniprot description
annotation
function
visualisation
bulk
NCBI
Uniprot
RNA
4 hours ago by
Amélie
• 0
0
votes
0
replies
92
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 19 hours ago by
Ram
43k • written 20 hours ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 17 hours ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
2
votes
1
reply
103
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 21 hours ago by
ATpoint
81k • written 22 hours ago by
catherine.teyssier
• 0
2
votes
3
replies
155
views
from row count to tpm
tpm
row-count
normalization
6 hours ago by
michelafrancesconi9
▴ 20
0
votes
0
replies
67
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 22 hours ago by
GenoMax
141k • written 22 hours ago by
Abeer
• 0
1
vote
4
replies
158
views
Downsampling fastq file
downsample
fastq
updated 22 hours ago by
Ram
43k • written 23 hours ago by
marco.barr
▴ 60
2
votes
3
replies
293
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 22 hours ago by
dsull
★ 5.8k • written 13 days ago by
javanokendo
▴ 60
0
votes
1
reply
107
views
tbtool
tbtool
updated 22 hours ago by
Ram
43k • written 23 hours ago by
Raman
• 0
0
votes
2
replies
157
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 20 hours ago by
i.sudbery
19k • written 23 hours ago by
Patadu94
• 0
3
votes
3
replies
178
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
130
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 19 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
emmanouil.a
▴ 120
0
votes
1
reply
100
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 1 day ago by
ATpoint
81k • written 1 day ago by
enanoide
• 0
0
votes
0
replies
72
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
1 day ago by
manaswwm
▴ 490
3
votes
3
replies
700
views
KissDE and batch effect
kissDE
kissplice
1 day ago by
david.b.rombaut
▴ 10
0
votes
0
replies
63
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
3 hours ago by
alifafiq1
• 0
76
votes
71
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 1 day ago by
GenoMax
141k • written 6.2 years ago by
Kevin Blighe
87k
0
votes
0
replies
73
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
1 day ago by
feather-W
• 0
116,558 results • Page
1 of 2332
Recent Votes
Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
The Biostar Herald for Monday, April 15, 2024
The Biostar Herald for Monday, April 15, 2024
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Fast way to extract specific sequences from large fasta
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141k
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Recent Replies
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
njornet
▴ 20
Ok thank you! Do you know if there is an easy way of doing so with ncbi-genome-download or I need to use another tool?
Comment: Using vg gamsort with naive sorting algorithm
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
The scope is all publications related to grants from an NIH award program. There are currently ~120k publications in total (about a few hun…
Answer: Using vg gamsort with naive sorting algorithm
by
anovak
▴ 110
The `-d` sorting mode does the entire sort in memory, so it will only work if you have enough memory to load your whole GAM file. To fin…
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
I have a list of PMIDs for publications linked to a list of grants, exported from NIH RePORTER.
Comment: Plot DNA methylation level of DMR on the basis of certain genes
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
GenoMax
141k
Yes you can remove those if you are only interested in annotated genes.
Comment: Help for coding: Trinity for differential gene expression studies
by
mchour
• 0
[This could help][1] [1]: https://github.com/trinityrnaseq/RNASeq_Trinity_Tuxedo_Workshop/wiki/Trinity-De-novo-Transcriptome-Assembly-W…
Answer: How to compare the quality of assemblies
by
colindaven
6.4k
Are you sure you have looked into the HiFiasm output files (fasta and GFA) in detail and excluded non-primary contigs, hap1, hap2 and other…
Answer: How to identify gaps in a genome?
by
colindaven
6.4k
You can use seqtk to find gaps in a fasta https://github.com/lh3/seqtk seqtk gap Usage: seqtk gap [-l 50] <in.fa>
Comment: some error in building kraken2 database
by
GenoMax
141k
> Obviously, running kraken2 after the build is complete does not produce the correct results What do you get instead? Error/no output? Ha…
Comment: Failed kmer content
by
GenoMax
141k
Can you post a screenshot of what you are referring to? Why did you choose to "clean" your data? FastQC analysis needs to be done keeping…
Comment: Help for coding: Trinity for differential gene expression studies
by
rhossen
• 0
It should be great if I have any assistance in my build up command using trinity package...
Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over
by
WouterDeCoster
47k
I want reads in a specific short interval, but if I do that with samtools view I also get reads that are spliced over that interval.
Answer: Help for coding: Trinity for differential gene expression studies
by
mchour
• 0
Hello, I would recommend following RSEM wiki for more information about the options, or even run RSEM directly, not with the script provi…
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