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188 results • Page
1 of 4
Sort: replies
Rank
Views
Votes
Replies
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
3 days ago by
vytarasov
▴ 180
13
votes
14
replies
880
views
High Malat-1 expression in single cell data
single-cell
updated 6 days ago by
t.montserrat.ayuso
▴ 40 • written 15 days ago by
carolofharvest
▴ 40
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 6 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 4 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 5 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
0
votes
11
replies
492
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
1 day ago by
Tuck898
• 0
1
vote
9
replies
364
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 4 days ago by
i.sudbery
19k • written 7 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 5 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
2
votes
8
replies
320
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
Matteo Ungaro
▴ 100
0
votes
8
replies
427
views
Different output for read length
samtools
BAM
4 days ago by
marco.barr
▴ 110
6
votes
7
replies
340
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
1 day ago by
sansan_96
▴ 90
0
votes
7
replies
401
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 1 day ago by
Mohamed Abderrahmane
▴ 20 • written 15 days ago by
matteo.levorato
• 0
4
votes
7
replies
380
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
17 hours ago by
Chen
• 0
1
vote
7
replies
511
views
Question regarding WGCNA
WGCNA
Network-construction
5 days ago by
deepak
• 0
9
votes
7
replies
7.1k
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
1
vote
7
replies
590
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 4 days ago by
Pierre Lindenbaum
161k • written 7 days ago by
schmince
• 0
0
votes
7
replies
497
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 6 days ago by
Wayne
★ 2.0k • written 7 days ago by
JACKY
▴ 140
3
votes
6
replies
472
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 1 day ago by
Pine
▴ 20 • written 9 days ago by
snajafy
• 0
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 6 days ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
0
votes
6
replies
377
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 20 hours ago by
Ram
43k • written 3 days ago by
ajbarrett98
• 0
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 5 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
0
votes
6
replies
190
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
1 hour ago by
ntsopoul
▴ 60
4
votes
6
replies
402
views
RNA seq analysis
DESeq
RNA-seq
updated 1 day ago by
Matthias Zepper
4.6k • written 6 days ago by
prifa
▴ 10
0
votes
5
replies
308
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
1 day ago by
feather-W
• 0
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 6 days ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
2
votes
5
replies
198
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 13 hours ago by
Philipp Bayer
8.5k • written 17 hours ago by
林明德
• 0
0
votes
5
replies
308
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
6 days ago by
me
• 0
1
vote
5
replies
351
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 6 days ago by
Michael
54k • written 7 days ago by
qwertyuiop26
• 0
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS
insertion site
trangene
de-novo
soap
updated 6 days ago by
Cameron.walker9900
• 0 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
1
vote
5
replies
433
views
HCL database download
HCL
updated 6 days ago by
Ram
43k • written 10 days ago by
sooni
▴ 20
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 2 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
2
votes
5
replies
387
views
Importing a fastq file
Fastq
updated 4 days ago by
size_t
▴ 120 • written 5 days ago by
oumo
• 0
0
votes
5
replies
256
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 6 days ago by
Joe
21k • written 6 days ago by
Lemonhope
• 0
5
votes
5
replies
292
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
6 days ago by
Chris
▴ 280
2
votes
5
replies
534
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
0
votes
5
replies
295
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
1 day ago by
SilhouetteQ
• 0
0
votes
4
replies
358
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
1 day ago by
beginner123
• 0
1
vote
4
replies
488
views
cellranger error message
multiplexing
cellranger
updated 4 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
2
votes
4
replies
271
views
BWA alignment
Samtools
bam
updated 10 hours ago by
ATpoint
82k • written 1 day ago by
Vahid
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 19 hours ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 6 days ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.5k
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
2
votes
4
replies
146
views
Help with IGV abbreviation
Genome
browser
17 hours ago by
GeneC
• 0
1
vote
4
replies
400
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 3 days ago by
GenoMax
142k • written 27 days ago by
aniigodwinn
• 0
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 1 day ago by
Thind amarinder
▴ 340 • written 4.9 years ago by
garbuzov
▴ 70
1
vote
4
replies
370
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 21 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
3
votes
4
replies
300
views
Truncated metadata file report from ENA Portal API
ena
python
3 days ago by
Giulia
• 0
1
vote
4
replies
376
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
6 days ago by
heelpPlease
• 0
0
votes
4
replies
285
views
Correlation Analysis
statistics
methylation
NGS
expression
3 days ago by
Researcher
▴ 30
1
vote
4
replies
324
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 20 hours ago by
Ram
43k • written 5 days ago by
samRayne
• 0
188 results • Page
1 of 4
Recent Votes
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Help with IGV abbreviation
Split multiallelic SNPs to biallelic from vcf
Filtering multi-allelic sites in VCF files
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Recent Replies
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data
by
GenoMax
142k
You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file
by
ramiro.barrantes
• 0
Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
Answer: RNAseq RNA content
by
ntsopoul
▴ 60
I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which …
Comment: RNAseq RNA content
by
ATpoint
82k
What is "row RNA"?
Comment: Overlapping Ranges within Granges object
by
ATpoint
82k
I would probably collapse overlapping regions with `reduce` to create the second GRanges. Can you add some representative data? Using dput?
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
by
J.
▴ 40
FYI if you also have this problem, this seems to be a pretty good solution: https://github.com/harvardinformatics/degenotate
Comment: Biomart issue, why so few 3'utrs?
by
GenoMax
142k
AFAIK "MANE" project is only for human protein-coding genes. One potential explanation. Out of the 2000 ID's only 125 may be MANE. https:…
Answer: Biomart issue, why so few 3'utrs?
by
i.sudbery
19k
The MANE-select transcripts are pairs of identically annotated transcripts in ReqSeq and Ensembl. The 3' UTR is the region where otherwise …
Comment: sci-RNA-seq
by
ATpoint
82k
Please understand that this impossibly can be answered without any code or plots, or details in general. "Hey my car does not start, it mak…
Comment: Biomart issue, why so few 3'utrs?
by
i.sudbery
19k
Which species is this?
Comment: How to access GWAVA software of data
by
GenoMax
142k
Please email the author (grsr at ebi.ac.uk) and let them know that the link above is not available.
Comment: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
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