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44 results • Page
1 of 1
Sort: Votes
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Views
Votes
Replies
5
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
6 hours ago by
Arton
• 0
4
votes
7
replies
435
views
RNA seq analysis
DESeq
RNA-seq
2 hours ago by
Jacek
▴ 10
4
votes
1
reply
171
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
21 hours ago by
J.
▴ 40
2
votes
4
replies
191
views
Help with IGV abbreviation
igv
updated 14 hours ago by
Ram
43k • written 1 day ago by
GeneC
• 0
2
votes
3
replies
268
views
Finding variants within a subset of a BAM file
variant
calling
19 hours ago by
ramiro.barrantes
• 0
2
votes
6
replies
344
views
BWA alignment
Samtools
bam
updated 5 hours ago by
a.alnawfal.1992
▴ 260 • written 2 days ago by
Vahid
• 0
2
votes
2
replies
160
views
Genome Visualization Tools
bacterial
genome
updated 15 hours ago by
GenoMax
142k • written 15 hours ago by
dlera.lozano
▴ 10
2
votes
9
replies
646
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 3 hours ago by
Pierre Lindenbaum
161k • written 7 days ago by
schmince
• 0
2
votes
4
replies
257
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
4 hours ago by
Esraa
• 0
1
vote
1
reply
134
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 2 hours ago by
dariober
14k • written 1 day ago by
Holly
▴ 10
1
vote
4
replies
323
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
1
vote
3
replies
162
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 14 hours ago by
Ram
43k • written 15 hours ago by
Prawesh
• 0
1
vote
5
replies
465
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 14 hours ago by
Ram
43k • written 6 days ago by
Prawesh
• 0
1
vote
2
replies
129
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 4 hours ago by
colindaven
6.4k • written 11 hours ago by
mbrav005
• 0
1
vote
7
replies
343
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
7 hours ago by
ntsopoul
▴ 60
1
vote
1
reply
116
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 17 hours ago by
Ram
43k • written 22 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
36
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmap
bbmerge
4 hours ago by
chrisk
• 0
0
votes
2
replies
132
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
3 hours ago by
melissa.joubert
• 0
0
votes
0
replies
30
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
3 hours ago by
Transmitting Science communication
▴ 70
0
votes
8
replies
528
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
3 hours ago by
JACKY
▴ 140
0
votes
0
replies
30
views
ReactomeGSA
ReactomeGSA
3 hours ago by
Shaimaa Gamal
▴ 10
0
votes
1
reply
75
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
updated 3 hours ago by
Pierre Lindenbaum
161k • written 6 hours ago by
Arton
• 0
0
votes
1
reply
48
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 1 hour ago by
ATpoint
82k • written 2 hours ago by
Alexandra
• 0
0
votes
0
replies
16
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
41 minutes ago by
egascon
• 0
0
votes
3
replies
33
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
23 minutes ago by
Esraa
• 0
0
votes
1
reply
53
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
updated 22 minutes ago by
marco.barr
▴ 110 • written 4 hours ago by
njornet
▴ 20
0
votes
0
replies
6
views
Annotating file using bcftools
annotation
plink
bcftools
13 minutes ago by
kl
▴ 10
0
votes
3
replies
178
views
How to access GWAVA software of data
GWAVA
updated 22 hours ago by
GenoMax
142k • written 1 day ago by
nonaddldy
▴ 10
0
votes
0
replies
9
views
genome finishing
finishing
genome
9 minutes ago by
trezini
• 0
0
votes
0
replies
75
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 22 hours ago by
GenoMax
142k • written 22 hours ago by
Bhavya
• 0
0
votes
3
replies
178
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 21 hours ago by
GenoMax
142k • written 1 day ago by
RNAseqer
▴ 270
0
votes
0
replies
84
views
Is there a real ground truth for CNV data?
CNV
21 hours ago by
jennyp0706
• 0
0
votes
0
replies
82
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
18 hours ago by
ramiro.barrantes
• 0
0
votes
1
reply
114
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 17 hours ago by
LauferVA
4.2k • written 18 hours ago by
graeme.thorn
▴ 100
0
votes
3
replies
210
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 16 hours ago by
noodle
▴ 580 • written 20 hours ago by
doramora
▴ 10
0
votes
1
reply
130
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 16 hours ago by
GenoMax
142k • written 16 hours ago by
bioinfo
▴ 150
0
votes
1
reply
118
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 14 hours ago by
Ram
43k • written 1 day ago by
Emily
▴ 20
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 14 hours ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
1
reply
99
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
updated 13 hours ago by
Mensur Dlakic
★ 27k • written 13 hours ago by
MarcosCosta
• 0
0
votes
0
replies
48
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
9 hours ago by
brunofelicianodeomena
• 0
0
votes
0
replies
54
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 8 hours ago by
GenoMax
142k • written 9 hours ago by
Dude
• 0
0
votes
2
replies
179
views
Using ggplotly in R
ggplot
ggplotly
7 hours ago by
jen
▴ 10
0
votes
1
reply
95
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
7 hours ago by
sansan_96
▴ 90
0
votes
0
replies
51
views
Forum:
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
7 hours ago by
iqra
• 0
44 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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Recent Replies
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…
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
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