Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
189 results • Page
2 of 4
Sort: Rank
Rank
Views
Votes
Replies
1
vote
5
replies
468
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 16 hours ago by
Ram
43k • written 6 days ago by
Prawesh
• 0
1
vote
3
replies
418
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
1 day ago by
kalavattam
▴ 190
1
vote
2
replies
255
views
How to interpret infinite odds ratio?
statistics
1 day ago by
Lukas
• 0
1
vote
2
replies
166
views
Duplicated sequence samtools
bowtie2
samtools
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Moinuddin
• 0
0
votes
0
replies
100
views
reference-free assembly error assessment tools
assembly
1 day ago by
lagartija
▴ 160
2
votes
4
replies
269
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
6 hours ago by
Esraa
• 0
2
votes
0
replies
135
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
1 day ago by
Biostar
2.8k
0
votes
1
reply
133
views
Splitting Seurat object by sample layers
seurat
updated 1 day ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
0
votes
4
replies
237
views
Galaxy StringTie error
stringtie
galaxy
1 day ago by
trkfs
• 0
0
votes
0
replies
98
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
1 day ago by
atariw
▴ 10
0
votes
1
reply
144
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 2 days ago by
GenoMax
142k • written 2 days ago by
octpus616
▴ 100
1
vote
4
replies
326
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 11 hours ago by
Juke34
8.6k • written 2 days ago by
Vijith
▴ 30
0
votes
1
reply
152
views
consensus sequence calling
consensus
updated 1 day ago by
bk11
★ 2.4k • written 2 days ago by
Ghada
• 0
0
votes
3
replies
177
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 1 day ago by
Ram
43k • written 2 days ago by
yau
• 0
3
votes
2
replies
261
views
imputation through beagle
panel
beagle
reference
imputation
1 day ago by
analyst
▴ 50
0
votes
0
replies
85
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
2 days ago by
JACKY
▴ 140
0
votes
1
reply
506
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 2 days ago by
aw7
▴ 280 • written 25 days ago by
abhishekghadge
• 0
1
vote
1
reply
200
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 2 days ago by
aw7
▴ 280 • written 6 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
96
views
Reference panel of normals for ensembl named refgenome
Mutect2
2 days ago by
gernophil
▴ 80
1
vote
0
replies
90
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
2 days ago by
tomas4482
▴ 400
2
votes
6
replies
353
views
BWA alignment
Samtools
bam
updated 7 hours ago by
a.alnawfal.1992
▴ 260 • written 2 days ago by
Vahid
• 0
3
votes
2
replies
179
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 2 days ago by
ATpoint
82k • written 2 days ago by
jennyp0706
• 0
0
votes
1
reply
151
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 2 days ago by
Philipp Bayer
8.5k • written 2 days ago by
samRayne
• 0
0
votes
1
reply
237
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 1 day ago by
Ram
43k • written 5 days ago by
Nikki
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
186
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 2 days ago by
chrchang523
10k • written 7 days ago by
analyst
▴ 50
0
votes
0
replies
102
views
lncRNA
tcga
lncrna
2 days ago by
jain72744
▴ 10
0
votes
1
reply
231
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 5 days ago by
jain72744
▴ 10
2
votes
5
replies
548
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 2 days ago by
arctic
▴ 40 • written 11 days ago by
M.
▴ 30
1
vote
2
replies
346
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 1 day ago by
Ram
43k • written 2 days ago by
t.fortunato.asquini
• 0
2
votes
1
reply
245
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 2 days ago by
pjb39
▴ 210 • written 4 days ago by
beantkapoor16
▴ 10
0
votes
2
replies
199
views
Output file of samtools flagstat empty
samtools-flagstat
updated 2 days ago by
colindaven
6.4k • written 3 days ago by
ramendra.sarma
• 0
0
votes
0
replies
104
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
3 days ago by
BioinfGuru
★ 1.7k
2
votes
8
replies
345
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 2 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
119
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
3 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
224
views
input file in rmats
rmats
updated 3 days ago by
Mathew
▴ 140 • written 5 days ago by
Lambodarswain316
• 0
3
votes
3
replies
339
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 1 day ago by
Mathew
▴ 140 • written 4 days ago by
Christopher
• 0
6
votes
7
replies
364
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
2 days ago by
sansan_96
▴ 90
2
votes
3
replies
260
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
2 days ago by
Azra
▴ 10
2
votes
1
reply
225
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
melissachua90
▴ 70
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 4 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
0
votes
4
replies
376
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
2 days 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 4 days ago by
Ruqaiya
• 0 • written 6.4 years ago by
dllopezr
▴ 130
0
votes
2
replies
222
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
2 days ago by
analyst
▴ 50
0
votes
6
replies
393
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 1 day ago by
Ram
43k • written 4 days ago by
ajbarrett98
• 0
0
votes
11
replies
510
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
2 days ago by
Tuck898
• 0
3
votes
3
replies
268
views
what is another word for a BLAST "hit"?
blast
alignment
4 days ago by
dec986
▴ 380
0
votes
1
reply
197
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 4 days ago by
Ram
43k • written 4 days ago by
Shwetha
• 0
0
votes
0
replies
159
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 4 days ago by
Ram
43k • written 4 days ago by
naomiboldon
• 0
1
vote
3
replies
271
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 4 days ago by
Ram
43k • written 4 days ago by
Omics data mining
▴ 260
189 results • Page
2 of 4
Recent Votes
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
Recent Locations •
All
France,
just now
United States,
1 minute ago
Belarus,
1 minute ago
France/Nantes/Institut du Thorax - INSERM UMR1087,
2 minutes ago
United States,
3 minutes ago
India,
4 minutes ago
outer space,
4 minutes ago
Recent Awards •
All
Popular Question
to
rj.rezwan
• 0
Popular Question
to
matteo.levorato
• 0
Popular Question
to
Palgrave
▴ 110
Popular Question
to
DBScan
▴ 300
Popular Question
to
chrisk
• 0
Popular Question
to
mbrav005
• 0
Popular Question
to
Sofia
• 0
Recent Replies
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
Thanks for the link. We never use "pod5_fail" folders when re-basecalling so we did not see this issue. Current version of MinKNOW now make…
Answer: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
with `findOverlaps` function in `GenomicRanges` package or directly with this package `GeneOverlap`. Check out the documentation of these …
Comment: Annotating file using bcftools
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…
Answer: Annotating file using bcftools
by
Pierre Lindenbaum
161k
I think your're annotating $REF/All_20180423.vcf.gz (DBSNP isn't it ? = no genotype) with your vcf as the database ro_imputed_hrcgrch37.R2_…
Comment: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
I had the same problem in this iusse [https://github.com/nanoporetech/dorado/issues/603][1] and I solved it as they say here [1]: https…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
ATpoint
82k
Looking at this briefly, it is small sample size and you do not correct for any potential confounders. Use PCA or MDS to explore the data. …
Comment: bbmerge (bbmap) ~ error with insert size file output
by
GenoMax
142k
> It is confirmed (and solved in another thread) that we have significant overlapping paired end reads. Can you provide a reference to sai…
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
> I get the exact same read with the same ID and all more than once If you have short(er) reads you could be seeing secondary alignments. …
Answer: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
Hi, I'm also working with ONT data and with dorado. From experience I tell you that some versions of MInKNOW have bad management of fast5 f…
Comment: Problem with Calling Variants from RNA-Seq data
by
Esraa
• 0
Yes, i specifically ran the RNA-seq best practices, and no i have not taken RNA editing into account considering this is not mentioned in t…
Comment: Problem with Calling Variants from RNA-Seq data
by
i.sudbery
19k
Have you accounted for A>I RNA editing?
Comment: Problem with Calling Variants from RNA-Seq data
by
Esraa
• 0
**My references** Genome: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_no_al…
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
by
ATpoint
82k
This has formally been investiated by a reputable group here: https://academic.oup.com/nar/article/42/11/e95/1442937 IIRC they think tha…
Comment: RNA seq analysis
by
Jacek
▴ 10
Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
by
dariober
14k
> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Traffic: 2711 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6