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116,939 results • Page
2 of 2339
Sort: Rank
Rank
Views
Votes
Replies
2
votes
4
replies
244
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
3 hours ago by
Esraa
• 0
2
votes
0
replies
133
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
1 day ago by
Biostar
2.8k
0
votes
1
reply
130
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
232
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
143
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 1 day ago by
GenoMax
142k • written 2 days ago by
octpus616
▴ 100
1
vote
4
replies
321
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 9 hours ago by
Juke34
8.6k • written 1 day ago by
Vijith
▴ 30
0
votes
1
reply
149
views
consensus sequence calling
consensus
updated 1 day ago by
bk11
★ 2.4k • written 1 day ago by
Ghada
• 0
0
votes
3
replies
173
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 1 day ago by
yau
• 0
3
votes
2
replies
258
views
imputation through beagle
panel
beagle
reference
imputation
1 day ago by
analyst
▴ 50
0
votes
0
replies
84
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
1 day ago by
JACKY
▴ 140
0
votes
1
reply
501
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 1 day 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 1 day 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
341
views
BWA alignment
Samtools
bam
updated 4 hours ago by
a.alnawfal.1992
▴ 260 • written 2 days ago by
Vahid
• 0
3
votes
2
replies
177
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
236
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 23 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
185
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
101
views
lncRNA
tcga
lncrna
2 days ago by
jain72744
▴ 10
0
votes
1
reply
230
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
546
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
345
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
243
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
197
views
Output file of samtools flagstat empty
samtools-flagstat
updated 2 days ago by
colindaven
6.4k • written 2 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
2 days ago by
BioinfGuru
★ 1.7k
2
votes
8
replies
342
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
333
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 3 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 3 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 3 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
391
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
507
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
196
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
9
votes
6
replies
12k
views
samtools tview symbols
samtools
updated 8.8 years ago by
Ashutosh Pandey
12k • written 8.8 years ago by
biolab
★ 1.4k
2
votes
9
replies
640
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 2 hours ago by
Pierre Lindenbaum
161k • written 7 days ago by
schmince
• 0
0
votes
5
replies
305
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
1 day ago by
SilhouetteQ
• 0
0
votes
1
reply
182
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 4 days ago by
GenoMax
142k • written 4 days ago by
maria.soler
• 0
0
votes
2
replies
280
views
How are score_weights calculated in this code?
single-cell
4 days ago by
carolofharvest
▴ 40
116,939 results • Page
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Recent Votes
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
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
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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…
Comment: Filtering Multi-sample VCF file for all except one Genotype
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: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
Comment: Applying the metacell2 algorithm using python
by
JACKY
▴ 140
I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data
by
melissa.joubert
• 0
Thank you! This was going to be my next option - to simply use the Read_1 libraries for all samples. Can I ask about the second option you…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
Thanks, that was exactly what i needed
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
Esraa
• 0
Thank you! I will try searching for this more and see if it would fit my analysis purposes.
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
Esraa
• 0
Thank you so much for answering! I actually found some studies doing it the way you mentioned. I ran the GATK best practices pipeline on t…
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
that's great, but i believe the issue is related to stdin rather than index
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
it is not!!
Comment: How to calculate coverage of Nanopore long read data?
by
Arton
• 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
mbrav005
• 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon
by
sansan_96
▴ 90
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