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12,764 results • Page
3 of 256
Sort: Rank
Rank
Views
Votes
Replies
1
vote
2
replies
175
views
Duplicated sequence samtools
bowtie2
samtools
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Moinuddin
• 0
0
votes
0
replies
104
views
reference-free assembly error assessment tools
assembly
3 days ago by
lagartija
▴ 160
2
votes
4
replies
291
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
1 day ago by
Esraa
• 0
2
votes
0
replies
140
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
3 days ago by
Biostar
2.8k
0
votes
1
reply
141
views
Splitting Seurat object by sample layers
seurat
updated 3 days ago by
Ram
43k • written 3 days ago by
kilcdincer
▴ 10
0
votes
4
replies
254
views
Galaxy StringTie error
stringtie
galaxy
2 days ago by
trkfs
• 0
0
votes
0
replies
102
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
3 days ago by
atariw
▴ 10
0
votes
1
reply
151
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 3 days ago by
GenoMax
142k • written 3 days ago by
octpus616
▴ 100
1
vote
4
replies
340
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 2 days ago by
Juke34
8.6k • written 3 days ago by
Vijith
▴ 30
0
votes
1
reply
161
views
consensus sequence calling
consensus
updated 3 days ago by
bk11
★ 2.4k • written 3 days ago by
Ghada
• 0
0
votes
3
replies
188
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 3 days ago by
Ram
43k • written 3 days ago by
yau
• 0
3
votes
2
replies
274
views
imputation through beagle
panel
beagle
reference
imputation
2 days ago by
analyst
▴ 50
0
votes
0
replies
87
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
3 days ago by
JACKY
▴ 140
0
votes
1
reply
527
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 3 days ago by
aw7
▴ 300 • written 27 days ago by
abhishekghadge
• 0
3
votes
1
reply
213
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 3 days ago by
aw7
▴ 300 • written 8 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
101
views
Reference panel of normals for ensembl named refgenome
Mutect2
3 days ago by
gernophil
▴ 80
1
vote
0
replies
95
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
3 days ago by
tomas4482
▴ 400
2
votes
6
replies
375
views
BWA alignment
Samtools
bam
updated 1 day ago by
a.alnawfal.1992
▴ 260 • written 4 days ago by
Vahid
• 0
3
votes
2
replies
186
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 3 days ago by
ATpoint
82k • written 3 days ago by
jennyp0706
• 0
0
votes
1
reply
156
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 3 days ago by
Philipp Bayer
8.5k • written 4 days ago by
samRayne
• 0
0
votes
1
reply
244
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 3 days ago by
Ram
43k • written 7 days ago by
Nikki
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 2 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
193
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 3 days ago by
chrchang523
10k • written 8 days ago by
analyst
▴ 50
0
votes
0
replies
109
views
lncRNA
tcga
lncrna
3 days ago by
jain72744
▴ 10
0
votes
1
reply
242
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 6 days ago by
jain72744
▴ 10
2
votes
5
replies
564
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 4 days ago by
arctic
▴ 40 • written 13 days ago by
M.
▴ 30
1
vote
2
replies
356
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 days ago by
Ram
43k • written 4 days ago by
t.fortunato.asquini
• 0
2
votes
1
reply
256
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 4 days ago by
pjb39
▴ 210 • written 6 days ago by
beantkapoor16
▴ 10
0
votes
2
replies
206
views
Output file of samtools flagstat empty
samtools-flagstat
updated 3 days ago by
colindaven
6.4k • written 4 days ago by
ramendra.sarma
• 0
2
votes
8
replies
368
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
127
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
4 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
229
views
input file in rmats
rmats
updated 4 days ago by
Mathew
▴ 140 • written 6 days ago by
Lambodarswain316
• 0
3
votes
3
replies
356
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 3 days ago by
Mathew
▴ 140 • written 6 days ago by
Christopher
• 0
6
votes
7
replies
382
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
4 days ago by
sansan_96
▴ 90
2
votes
3
replies
276
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
3 days ago by
Azra
▴ 10
2
votes
1
reply
231
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 5 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
melissachua90
▴ 70
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 5 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
0
votes
4
replies
392
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
3 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 5 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
0
votes
2
replies
228
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
3 days ago by
analyst
▴ 50
0
votes
6
replies
417
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 3 days ago by
Ram
43k • written 6 days ago by
ajbarrett98
• 0
0
votes
11
replies
531
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
4 days ago by
Tuck898
• 0
3
votes
3
replies
278
views
what is another word for a BLAST "hit"?
blast
alignment
6 days ago by
dec986
▴ 380
0
votes
1
reply
202
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 6 days ago by
Ram
43k • written 6 days ago by
Shwetha
• 0
0
votes
0
replies
163
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 6 days ago by
Ram
43k • written 6 days ago by
naomiboldon
• 0
1
vote
3
replies
281
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 6 days ago by
Ram
43k • written 6 days ago by
Omics data mining
▴ 260
2
votes
9
replies
690
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 1 day ago by
Pierre Lindenbaum
161k • written 9 days ago by
schmince
• 0
0
votes
5
replies
316
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
3 days ago by
SilhouetteQ
• 0
0
votes
1
reply
187
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 6 days ago by
GenoMax
142k • written 6 days ago by
maria.soler
• 0
0
votes
2
replies
291
views
How are score_weights calculated in this code?
single-cell
5 days ago by
carolofharvest
▴ 40
12,764 results • Page
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Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Answer: Details on salmon index
ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Can I perform a correlation test with 3 biological replicates per condition?
Answer: --normalizeUsing RPGC
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Comment: Sam file Header problem
by
saifulislam99121
• 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite
by
dario.garvan
▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
GenoMax
142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo.
by
Ram
43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
txema.heredia
▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
swbarnes2
14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
Comment: Help with VG Toolkit: VCF Output is Empty
by
Jordan M Eizenga
▴ 460
What do you get if you use `vg stats -a` on the GAM file?
Comment: About runing Pilon on individual chromosomes when polish draft genome assembly
by
sansan_96
▴ 90
Hello, What approach could you recommend for a large genome (3Gb) with about 10k scaffolds? I'm having problems with RAM when processing t…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
e.r.zakiev
▴ 210
Very good question and analysis. I personally only tried SoupX so can't weigh in on the comparison. This might be not really the issue here…
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