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40 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
8
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
20 minutes ago by
njornet
▴ 20
0
votes
0
replies
9
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmap
bbmerge
40 minutes ago by
chrisk
• 0
0
votes
0
replies
31
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
2 hours ago by
Arton
• 0
0
votes
0
replies
28
views
Forum:
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
2 hours ago by
iqra
• 0
0
votes
0
replies
39
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 4 hours ago by
GenoMax
142k • written 5 hours ago by
Dude
• 0
0
votes
0
replies
41
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
5 hours ago by
brunofelicianodeomena
• 0
1
vote
2
replies
99
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated just now by
colindaven
6.4k • written 7 hours ago by
mbrav005
• 0
0
votes
1
reply
74
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
2 hours ago by
sansan_96
▴ 90
0
votes
1
reply
85
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
updated 8 hours ago by
Mensur Dlakic
★ 27k • written 9 hours ago by
MarcosCosta
• 0
2
votes
2
replies
143
views
Genome Visualization Tools
bacterial
genome
updated 10 hours ago by
GenoMax
142k • written 10 hours ago by
dlera.lozano
▴ 10
1
vote
3
replies
148
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 10 hours ago by
Ram
43k • written 11 hours ago by
Prawesh
• 0
0
votes
2
replies
149
views
Using ggplotly in R
ggplot
ggplotly
3 hours ago by
jen
▴ 10
0
votes
1
reply
117
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 11 hours ago by
GenoMax
142k • written 12 hours ago by
bioinfo
▴ 150
0
votes
3
replies
200
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 12 hours ago by
noodle
▴ 580 • written 16 hours ago by
doramora
▴ 10
0
votes
1
reply
103
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 13 hours ago by
LauferVA
4.2k • written 14 hours ago by
graeme.thorn
▴ 100
0
votes
1
reply
100
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
updated 13 hours ago by
GenoMax
142k • written 14 hours ago by
melissa.joubert
• 0
0
votes
0
replies
72
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
14 hours ago by
ramiro.barrantes
• 0
4
votes
1
reply
163
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
16 hours ago by
J.
▴ 40
0
votes
0
replies
74
views
Is there a real ground truth for CNV data?
CNV
17 hours ago by
jennyp0706
• 0
0
votes
3
replies
169
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 17 hours ago by
GenoMax
142k • written 1 day ago by
RNAseqer
▴ 270
1
vote
1
reply
106
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 13 hours ago by
Ram
43k • written 17 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
65
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 18 hours ago by
GenoMax
142k • written 18 hours ago by
Bhavya
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 20 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
7
replies
318
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
3 hours ago by
ntsopoul
▴ 60
0
votes
3
replies
167
views
How to access GWAVA software of data
GWAVA
updated 18 hours ago by
GenoMax
142k • written 21 hours ago by
nonaddldy
▴ 10
1
vote
1
reply
140
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 22 hours ago by
ATpoint
82k • written 1 day ago by
Pegasus
▴ 100
0
votes
1
reply
107
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 9 hours ago by
Ram
43k • written 1 day ago by
Emily
▴ 20
1
vote
1
reply
156
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 23 hours ago by
zx8754
11k • written 1 day ago by
ohtang7
▴ 40
0
votes
2
replies
148
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
22 hours ago by
IdaHao0921
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 9 hours ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
183
views
Help with IGV abbreviation
igv
updated 9 hours ago by
Ram
43k • written 1 day ago by
GeneC
• 0
1
vote
5
replies
448
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 10 hours ago by
Ram
43k • written 6 days ago by
Prawesh
• 0
1
vote
2
replies
243
views
How to interpret infinite odds ratio?
statistics
20 hours ago by
Lukas
• 0
0
votes
4
replies
227
views
Galaxy StringTie error
stringtie
galaxy
20 hours ago by
trkfs
• 0
1
vote
4
replies
297
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 5 hours ago by
Juke34
8.6k • written 1 day ago by
Vijith
▴ 30
3
votes
2
replies
257
views
imputation through beagle
panel
beagle
reference
imputation
23 hours ago by
analyst
▴ 50
2
votes
6
replies
310
views
BWA alignment
Samtools
bam
updated 1 hour ago by
a.alnawfal.1992
▴ 260 • written 2 days ago by
Vahid
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 20 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
2
votes
3
replies
267
views
Finding variants within a subset of a BAM file
variant
calling
14 hours ago by
ramiro.barrantes
• 0
5
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
2 hours ago by
Arton
• 0
40 results • Page
1 of 1
Recent Votes
Comment: Bamutils/ClipOverlap
Comment: How to calculate coverage of Nanopore long read data?
Comment: Overlapping Ranges within Granges object
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
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Recent Awards •
All
Popular Question
to
DBScan
▴ 300
Popular Question
to
chrisk
• 0
Popular Question
to
mbrav005
• 0
Popular Question
to
Sofia
• 0
Popular Question
to
jen
▴ 10
Popular Question
to
nitinra
▴ 50
Scholar
to
Pierre Lindenbaum
161k
Recent Replies
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
..........
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R
by
jen
▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Juke34
8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
Mensur Dlakic
★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools
by
dlera.lozano
▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat
by
Mensur Dlakic
★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Ram
43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
• 0
thanks, it's working now.
Answer: Genome Visualization Tools
by
GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
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