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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
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
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
507
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
2 days ago by
Tuck898
• 0
2
votes
9
replies
633
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 1 hour ago by
Pierre Lindenbaum
161k • written 7 days ago by
schmince
• 0
1
vote
9
replies
374
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 6 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
0
votes
8
replies
522
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
2 hours ago by
JACKY
▴ 140
0
votes
8
replies
434
views
Different output for read length
samtools
BAM
5 days ago by
marco.barr
▴ 110
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
1
vote
7
replies
340
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
6 hours ago by
ntsopoul
▴ 60
6
votes
7
replies
363
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
2 days ago by
sansan_96
▴ 90
0
votes
7
replies
408
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 2 days ago by
Mohamed Abderrahmane
▴ 20 • written 16 days ago by
matteo.levorato
• 0
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
4
votes
7
replies
425
views
RNA seq analysis
DESeq
RNA-seq
1 hour ago by
Jacek
▴ 10
4
votes
7
replies
385
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
1 day ago by
Chen
• 0
1
vote
7
replies
524
views
Question regarding WGCNA
WGCNA
Network-construction
5 days ago by
deepak
• 0
2
votes
6
replies
338
views
BWA alignment
Samtools
bam
updated 4 hours ago by
a.alnawfal.1992
▴ 260 • written 2 days ago by
Vahid
• 0
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
3
votes
6
replies
479
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 2 days 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
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
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
5
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
5 hours ago by
Arton
• 0
0
votes
5
replies
268
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 6 days ago by
Joe
21k • written 7 days ago by
Lemonhope
• 0
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
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
0
votes
5
replies
318
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
2 days ago by
feather-W
• 0
1
vote
5
replies
464
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 13 hours ago by
Ram
43k • written 6 days ago by
Prawesh
• 0
0
votes
5
replies
305
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
1 day ago by
SilhouetteQ
• 0
2
votes
5
replies
394
views
Importing a fastq file
Fastq
updated 5 days ago by
size_t
▴ 120 • written 6 days ago by
oumo
• 0
2
votes
5
replies
238
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 1 day ago by
Philipp Bayer
8.5k • written 1 day ago by
林明德
• 0
2
votes
5
replies
543
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
316
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
6 days ago by
me
• 0
1
vote
4
replies
492
views
cellranger error message
multiplexing
cellranger
updated 4 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
2
votes
4
replies
242
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
3 hours ago by
Esraa
• 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
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 8 hours ago by
Juke34
8.6k • written 1 day ago by
Vijith
▴ 30
0
votes
4
replies
374
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
2 days ago by
beginner123
• 0
0
votes
4
replies
232
views
Galaxy StringTie error
stringtie
galaxy
23 hours ago by
trkfs
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 23 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
0
votes
4
replies
295
views
Correlation Analysis
statistics
methylation
NGS
expression
4 days ago by
Researcher
▴ 30
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
2
votes
4
replies
190
views
Help with IGV abbreviation
igv
updated 13 hours ago by
Ram
43k • written 1 day ago by
GeneC
• 0
3
votes
4
replies
309
views
Truncated metadata file report from ENA Portal API
ena
python
4 days ago by
Giulia
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 1 day ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 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
404
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 4 days ago by
GenoMax
142k • written 27 days ago by
aniigodwinn
• 0
1
vote
4
replies
332
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 1 day ago by
Ram
43k • written 6 days ago by
samRayne
• 0
188 results • Page
1 of 4
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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