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120,514 results • Page
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12
views
low alignment rate for RNA-Seq data
rice
low
alignment
RNA-Seq
38 minutes ago by
analyst
▴ 60
0
votes
0
replies
18
views
Optimal Computer Configuration for Bioinformatics Analysis
scRNA-seq
computer
1 hour ago by
Song
▴ 10
0
votes
0
replies
35
views
Variant Missing in VCF but Present in BAM Files: Discrepancy Identified via IGV Report in Join-Call Project
GATK
Deepvariant
BWA
4 hours ago by
lunping98
• 0
0
votes
0
replies
30
views
no - strand in transcriptome alignment
DRS
transcriptome
alignment
4 hours ago by
baibhu1234
▴ 20
0
votes
0
replies
42
views
Anndata vs cloupe
seurat
cloupe
scanpy
anndata
6 hours ago by
Rika
• 0
0
votes
2
replies
82
views
Gene Mapping Issue
DAVID
5 hours ago by
won
• 0
828
votes
169
replies
168k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.2 years ago by
Istvan Albert
102k
0
votes
0
replies
53
views
Job:
Assistant, Associate, or Full Project Scientist in Molecular Biology
molecular
teaching
biology
8 hours ago by
UCSDBioSci
▴ 30
0
votes
2
replies
126
views
RNA variant calling - SNP and indels files
mouse
variant_calling
genomics
RNA
updated 9 hours ago by
swbarnes2
14k • written 20 hours ago by
Nerelys
• 0
2
votes
4
replies
137
views
Manta analysis in WES
Deletion
MANTA
WES
SV
Exomiser
11 hours ago by
Eduardo
• 0
0
votes
1
reply
72
views
All VS All contamination check for tumor samples
tumor
contamination
updated 14 hours ago by
ATpoint
87k • written 14 hours ago by
mps
• 0
1
vote
2
replies
104
views
Determine binding sites in unstimulated TF ChIP-seq samples
ChIP-seq
csaw
9 hours ago by
Jacek
▴ 20
0
votes
0
replies
88
views
GO analysis custom reference?
GO-analysis
updated 14 hours ago by
Ram
44k • written 17 hours ago by
Pit
• 0
0
votes
2
replies
129
views
Query on WES
WES
15 hours ago by
rauf.sania786
• 0
5
votes
15
replies
6.2k
views
9 follow
BLAST Database error: Database memory map file error
makeblastdb
updated 5 hours ago by
Mensur Dlakic
★ 29k • written 5 months ago by
Martina
• 0
0
votes
0
replies
75
views
News:
Introduction to Machine Learning in R online course
R
statistics
AI
machine-learning
updated 14 hours ago by
Ram
44k • written 19 hours ago by
Transmitting Science communication
▴ 70
4
votes
6
replies
318
views
Nanopore long-read sequencing doubts and problems
minmap2
long-reads
NanoPlot
Nanopore
updated 9 hours ago by
lieven.sterck
15k • written 1 day ago by
ferran.llobet
▴ 10
0
votes
0
replies
76
views
Query Regarding Missing Sample Paths in Graph-Based Pangenome Construction
pangenome
variant_calling
giraffe
vg
haplotypes
1 day ago by
s_135
▴ 10
1
vote
3
replies
219
views
cannot install GO.db in windows
GO.db
updated 21 hours ago by
i.sudbery
21k • written 1 day ago by
Naila
• 0
1
vote
5
replies
237
views
conda :FileNotFoundError: [Errno 2] No such file or directory
conda
updated 21 hours ago by
Mensur Dlakic
★ 29k • written 1 day ago by
JieQY
• 0
6
votes
5
replies
228
views
Samtools view only showing read2 for PE mapped reads
Samtools
mem2
bwa
flagstat
mapping
updated 1 day ago by
Pierre Lindenbaum
165k • written 1 day ago by
knickknack
• 0
0
votes
3
replies
229
views
Color AlphaFold PDB by B-Factor (pLDDT) in PyMol
pdb
pymol
updated 13 hours ago by
Mensur Dlakic
★ 29k • written 2 days ago by
Schmoho
▴ 10
2
votes
2
replies
199
views
How to Resolve Overlapping Peaks in Sanger Chromatograms?
sequence-analysis
sanger-sequencing
dna-sequencing
chromatogram
1 day ago by
JOSÉ
• 0
4
votes
7
replies
293
views
Manual conversion of VCF genotypes to nucleotide sequence
vcf
nucleotide
sequence
updated 1 day ago by
Ram
44k • written 2 days ago by
endretoth
▴ 40
2
votes
3
replies
301
views
How to remove rows with empty gene symbols from a seurat object?
seurat
updated 2 days ago by
Michael
55k • written 4 days ago by
Chris
▴ 360
4
votes
11
replies
573
views
7 follow
Phylogenetic tree from whole genome using BUSCO
BUSCO
whole_genome
phylogenetic_tree
updated 2 days ago by
colindaven
7.2k • written 5 days ago by
manaswiniparija3
▴ 60
0
votes
0
replies
135
views
News:
Course on Ancient Metagenomics - online, 27-29 May
ancientDNA
Metagenomics
aMeta
2 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
641
views
Difference between trim galore report and Fastqc pre trimming
trim-galore
updated 1 day ago by
Ram
44k • written 2.6 years ago by
Luern
• 0
0
votes
0
replies
165
views
From Cram to gVCF
Cram
gVCF
3 days ago by
heureuse
• 0
2
votes
4
replies
1.3k
views
R CytoTRACE2 Results: Potency Score of Naive B Cells Lower Than Memory B and Plasmablasts – Contradicts Biological Knowledge
CytoTRACE2
2 days ago by
Binghong
▴ 20
3
votes
1
reply
319
views
Rules for Assigning Start and End Phase to Coding Exons
stare_phase
reading_frame
end_phase
updated 3 days ago by
Jorge - Ensembl
▴ 10 • written 6 days ago by
Milica
▴ 20
0
votes
1
reply
189
views
converting transcript positions to genomic locations
genomic
locations
updated 3 days ago by
Pierre Lindenbaum
165k • written 3 days ago by
baibhu1234
▴ 20
0
votes
1
reply
226
views
Read groups RNA-seq and hisat2
hisat2
RNA-seq
read-groups
updated 3 days ago by
Ram
44k • written 3 days ago by
frarodmar17
• 0
0
votes
0
replies
162
views
simulate a genome with specific event
simulation
genome
retrocopy
3 days ago by
Matteo Ungaro
▴ 110
6
votes
4
replies
796
views
6 follow
Help with R programming assignment
R
offtopic
updated 2 days ago by
Michael
55k • written 7 months ago by
sidhanthbaru
• 0
0
votes
0
replies
160
views
HOMER findMotifsGenome.pl failed compilation
findMotifsGenome.pl
motifanalysis
HOMER
3 days ago by
India
• 0
1
vote
1
reply
248
views
Job:
SciLifeLab PULSE: Program for Future Leaders in Life Science (48 positions!)
Entrepreneur
Sweden
Mentoring
Postdoctoral
Leadership
3 days ago by
Matthias Zepper
5.0k
1
vote
1
reply
245
views
MSA with extended alphabet
Multiple
sequence
MSA
alignment
updated 3 days ago by
Mensur Dlakic
★ 29k • written 4 days ago by
retzl.bernhard
• 0
0
votes
0
replies
160
views
Help with Finding SNPs in H. pylori Assembled Genomes
question
Technical
3 days ago by
vrao
• 0
0
votes
2
replies
243
views
Reference Genome with decoy for RNAseq data processing
STAR
SALMON
RNAseq
updated 3 days ago by
Zhenyu Zhang
★ 1.2k • written 3 days ago by
cwwong13
▴ 40
1
vote
1
reply
226
views
multiple ATG SEQUENCE
MULTIPE
sequence
ATG
offtopic
updated 3 days ago by
Carlo Yague
8.9k • written 3 days ago by
Sijjil
• 0
0
votes
0
replies
175
views
Keep SNP's with call rate greater than 30 in VCF
SNP
call
rate
ROH
genotyping
updated 3 days ago by
Bastien Hervé
6.1k • written 4 days ago by
Smilesky
• 0
9
votes
10
replies
5.3k
views
7 follow
Buy PC for metagenomics
Assembly
alignment
genome
next-gen
updated 3 days ago by
Joe
22k • written 6.6 years ago by
lugonauta
▴ 10
0
votes
0
replies
166
views
Dynamic tree cut results
clustering
DEG
3 days ago by
Mai.Nabil
• 0
0
votes
0
replies
170
views
Significant variation in FastQ File Sizes - WES
LibraryPrep
WES
Human
4 days ago by
irate.pirate
• 0
0
votes
2
replies
353
views
Repetitive sequences analysis
Repetitive
sequences
updated 4 days ago by
rfran010
★ 1.4k • written 5 days ago by
frarodmar17
• 0
0
votes
1
reply
236
views
Protein secuence extraction from gpff file for a genes list
Protein
gpff
updated 4 days ago by
JC
13k • written 4 days ago by
reza
▴ 300
0
votes
0
replies
195
views
Job:
Postdoctoral Researcher in Single-Cell Sequencing Analysis
researcher
post-doctoral
4 days ago by
ejvandenoord
• 0
0
votes
2
replies
306
views
filtering heterozygous genotypes
bcftools
heterozygous
4 days ago by
analyst
▴ 60
2
votes
0
replies
255
views
An alternative to haplotype phasing - assembly?
samtools
assembly
BAM
spades
phasing
4 days ago by
Jess
▴ 60
120,514 results • Page
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Recent Votes
Comment: BLAST Database error: Database memory map file error
Answer: Nanopore long-read sequencing doubts and problems
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
A: How to calculate Minor Allele Frequency (MAF) for your own population data
A: How to calculate Minor Allele Frequency (MAF) for your own population data
Answer: allele frequency in VCF
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Recent Replies
Comment: Gene Mapping Issue
by
won
• 0
Hey, thanks for the advice! I get what you mean, and I usually try to include as much detail as possible. Right now, I’m working on RNA-se…
Comment: Gene Mapping Issue
by
lieven.sterck
15k
welcome https://www.biostars.org/u/149163/ , A word of advise to a newbie on the forum :) : do put some work in the posts you make. The mo…
Comment: BLAST Database error: Database memory map file error
by
Michael
55k
First, please don't do this, use [the update_blastdb.pl command][1]. Second, as to why this doesn't work this time: Because as of 2025-02-…
Comment: BLAST Database error: Database memory map file error
by
Mensur Dlakic
★ 29k
> I also should have enough memory. Anyone has some ideas to fix this issue? The only idea I have is that you don't have enough memory. Wh…
Answer: RNA variant calling - SNP and indels files
by
swbarnes2
14k
Known SNPs are probably more important for sequencing wild individuals, not pure-bred strains. It's not like you need to filter away known…
Comment: Nanopore long-read sequencing doubts and problems
by
JC
13k
That depends if the base call was done with a reference genome, so, the BAM could be with or without alignments.
Comment: Nanopore long-read sequencing doubts and problems
by
lieven.sterck
15k
more or less yes The BAM that is produced is just an alternative for the FASTQ files, and will become the new standard for ONT output fil…
Comment: Determine binding sites in unstimulated TF ChIP-seq samples
by
Jacek
▴ 20
hello thank you for your reply, can you clarify how to do the contrast for the untreated samples? here, what I would like to achieve is to …
Comment: BLAST Database error: Database memory map file error
by
lieven.sterck
15k
on a side note: if you download it directly from NCBI do also download the md5 checksum keys and use them to check the sanity of your downl…
Comment: Manta analysis in WES
by
Eduardo
• 0
Sorry, my bad. You are right. I forgot to check before using it in the exome data. It will not work...
Comment: Manta analysis in WES
by
Eduardo
• 0
Thank you so much! I didn't knew it. It help me a lot! Best regards, Eduardo.
Answer: Manta analysis in WES
by
GokalpC
▴ 110
Those het deletions are not really deletions. If you can take a look at in those variants with more detail you will see that those breakpoi…
Comment: Manta analysis in WES
by
Pierre Lindenbaum
165k
DUPHOLD for WES ? as duphold looks at the boundaries and you may not have captured those regions in the exome, I don't think that is the …
Comment: All VS All contamination check for tumor samples
by
ATpoint
87k
You really need to give details on the specimen. I assume we talk some NGS here, but how would we know?
Comment: Extract FUngal mRNA from RNAseq Data
by
SomeOne
▴ 170
Hey, @genomax I have another query regarding `bbaplit.sh`. As i have mentioned that the raw-reads are of RNASeq, is `bbsplit.sh` performi…
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