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13,181 results • Page
1 of 264
Sort: Rank
Rank
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Votes
Replies
1
vote
3
replies
258
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
19 minutes ago by
kalavattam
▴ 190
0
votes
1
reply
90
views
How to interpret infinite odds ratio?
statistics
updated 59 minutes ago by
bhumm
▴ 140 • written 6 hours ago by
Lukas
• 0
0
votes
2
replies
45
views
Duplicated sequence samtools
bowtie2
samtools
updated 1 hour ago by
GenoMax
142k • written 2 hours ago by
Moinuddin
• 0
0
votes
0
replies
23
views
reference-free assembly error assessment tools
assembly
2 hours ago by
lagartija
▴ 160
1
vote
2
replies
100
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 2 hours ago by
lagartija
▴ 160 • written 7 hours ago by
Esraa
• 0
1
vote
0
replies
31
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
2 hours ago by
J.
▴ 10
0
votes
0
replies
42
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
3 hours ago by
Biostar
2.7k
795
votes
167
replies
143k
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
50
views
Splitting Seurat object by sample layers
split
seuratobject
seurat
layers
updated 3 hours ago by
bk11
★ 2.4k • written 3 hours ago by
kilcdincer
▴ 10
0
votes
2
replies
66
views
Galaxy StringTie error
stringtie
troubleshoot
galaxy
error
3 hours ago by
trkfs
• 0
0
votes
0
replies
40
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
5 hours ago by
atariw
▴ 10
0
votes
1
reply
91
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 6 hours ago by
GenoMax
142k • written 16 hours ago by
octpus616
▴ 100
0
votes
1
reply
70
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 6 hours ago by
Juke34
8.6k • written 6 hours ago by
Vijith
▴ 30
0
votes
1
reply
76
views
consensus sequence calling
consensus
updated 3 hours ago by
bk11
★ 2.4k • written 7 hours ago by
Ghada
• 0
0
votes
3
replies
111
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
R
single-cell
RNA-seq
bioinformatics
8 hours ago by
yau
• 0
3
votes
2
replies
177
views
imputation through beagle
panel
beagle
reference
imputation
2 hours ago by
analyst
▴ 50
0
votes
0
replies
41
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
7 hours ago by
JACKY
▴ 140
0
votes
1
reply
323
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 8 hours ago by
aw7
▴ 280 • written 23 days ago by
abhishekghadge
• 0
1
vote
1
reply
159
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 8 hours ago by
aw7
▴ 280 • written 4 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
54
views
Reference panel of normals for ensembl named refgenome
Mutect2
9 hours ago by
gernophil
▴ 80
1
vote
0
replies
50
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
9 hours ago by
tomas4482
▴ 400
2
votes
3
replies
195
views
BWA alignment
Samtools
bam
10 hours ago by
Vahid
• 0
3
votes
2
replies
122
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 10 hours ago by
ATpoint
82k • written 10 hours ago by
jennyp0706
• 0
0
votes
1
reply
118
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 11 hours ago by
Philipp Bayer
8.4k • written 1 day ago by
samRayne
• 0
0
votes
1
reply
202
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization
Mendelian
two-sample
updated 11 hours ago by
Zeng Jingyu
▴ 60 • written 4 days ago by
Nikki
• 0
2
votes
13
replies
2.8k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 13 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
155
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 13 hours ago by
chrchang523
10k • written 5 days ago by
analyst
▴ 50
0
votes
0
replies
69
views
lncRNA
tcga
lncrna
14 hours ago by
jain72744
▴ 10
0
votes
1
reply
200
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 20 hours ago by
Zhenyu Zhang
★ 1.2k • written 3 days ago by
jain72744
▴ 10
2
votes
5
replies
504
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 1 day ago by
arctic
▴ 40 • written 10 days ago by
M.
▴ 30
1
vote
2
replies
288
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 3 hours ago by
Ram
43k • written 1 day ago by
t.fortunato.asquini
• 0
2
votes
1
reply
217
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 1 day ago by
pjb39
▴ 210 • written 3 days ago by
beantkapoor16
▴ 10
0
votes
2
replies
172
views
Output file of samtools flagstat empty
samtools-flagstat
updated 10 hours ago by
colindaven
6.4k • written 1 day ago by
ramendra.sarma
• 0
0
votes
0
replies
84
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
1 day ago by
BioinfGuru
★ 1.7k
2
votes
8
replies
297
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
101
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
208
views
input file in rmats
rmats
updated 1 day ago by
Mathew
▴ 120 • written 3 days ago by
Lambodarswain316
• 0
2
votes
2
replies
247
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
6 hours ago by
Christopher
• 0
6
votes
7
replies
324
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
1 day ago by
sansan_96
▴ 90
2
votes
3
replies
230
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
8 hours ago by
Azra
▴ 10
2
votes
1
reply
203
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
melissachua90
▴ 70
9
votes
7
replies
7.1k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 2 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
0
votes
4
replies
346
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
11 hours ago by
beginner123
• 0
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 2 days ago by
Ruqaiya
• 0 • written 6.4 years ago by
dllopezr
▴ 130
0
votes
2
replies
203
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
12 hours ago by
analyst
▴ 50
0
votes
6
replies
368
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
updated 1 day ago by
Pierre Lindenbaum
161k • written 2 days ago by
ajbarrett98
• 0
0
votes
11
replies
467
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
1 day ago by
Tuck898
• 0
3
votes
3
replies
246
views
what is another word for a BLAST "hit"?
blast
alignment
2 days ago by
dec986
▴ 380
0
votes
1
reply
188
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 2 days ago by
Ram
43k • written 2 days ago by
Shwetha
• 0
0
votes
0
replies
157
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 2 days ago by
Ram
43k • written 3 days ago by
naomiboldon
• 0
13,181 results • Page
1 of 264
Recent Votes
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
Practical Haplotype Graph v2 not finding correct paths
Extracting only 4-fold degenerate sites from gene sequences/alignments?
Producing sequence for splicing isoforms
How To Split A .Vcf.Gz File
Answer: imputation through beagle
Answer: imputation through beagle
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kalavattam
▴ 190
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dthorbur
★ 2.0k
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Santosh Anand
5.7k
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lagartija
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Recent Replies
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
kalavattam
▴ 190
> My question is this: "mate reverse strand" (flag 16/0x10) or "read reverse strand" (flag 32/0x20) do not directly relate to the strandedn…
Answer: How to interpret infinite odds ratio?
by
bhumm
▴ 140
As you stated, your problem is likely division by 0. See this [Cross-Validated][1] post that seems to be very similar to your problem. In …
Comment: Duplicated sequence samtools
by
GenoMax
142k
Consider using SLURM job arrays if you want to use a `for` loop inside a single SLURM job: https://hpc.nmsu.edu/discovery/slurm/job-arrays/
Answer: Duplicated sequence samtools
by
Pierre Lindenbaum
161k
the sequence c_000007023807_aloha2_low_cov is duplicated in the reference grep c_000007023807_aloha2_low_cov path/to/reference.fasta
Comment: imputation through beagle
by
analyst
▴ 50
Thank you so much dthorbur. Yes I am new to imputation analysis. I will follow your kind suggestions. Thanks again!
Answer: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
lagartija
▴ 160
I don't know but another way of doing it would be to combine different datasets of different strains that you know are clonal. Then you kno…
Comment: consensus sequence calling
by
bk11
★ 2.4k
Please check out these posts https://www.biostars.org/p/367626/
Comment: Galaxy StringTie error
by
trkfs
• 0
will do, thank you
Answer: Splitting Seurat object by sample layers
by
bk11
★ 2.4k
You can do the following- Idents(SeuratObj) <- "orig.ident" control_set <- subset(SeuratObj, idents = c("counts.control","data.…
Comment: Galaxy StringTie error
by
GenoMax
142k
> I have sent a bug report to the Galaxy administrator If you have not done so please post this in Galaxy help forum for directed help: h…
Comment: 44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped
by
Thind amarinder
▴ 340
Wondering, if it was total RNAseq data? or ployA
Comment: RNA seq analysis
by
Matthias Zepper
4.6k
It is still obscure to me how many different tissues you would like to include into your comparison and what your intended design is. To …
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Juke34
8.6k
You can get a look here https://www.biostars.org/p/9465973/
Answer: Mouse ribosome sequences in fasta format
by
GenoMax
142k
A version of the mouse rDNA repeat can be found here: https://www.ncbi.nlm.nih.gov/nuccore/BK000964 Use the dropdown menu at top-left t…
Comment: Kraken2 database
by
Christopher
• 0
Hello, Mathew. Firstly, thank you for answering my question. **Sorry, what analysis are you trying to perform with these databases?** I a…
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