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1,000 results • Page
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
2
votes
3
replies
211
views
from row count to tpm
tpm
row-count
normalization
6 days ago by
michelafrancesconi9
▴ 20
1
vote
6
replies
309
views
Downsampling fastq file
downsample
fastq
2 hours ago by
marco.barr
▴ 80
2
votes
3
replies
333
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 2 days ago by
dsull
★ 5.9k • written 19 days ago by
javanokendo
▴ 60
0
votes
1
reply
139
views
tbtool
tbtool
updated 6 days ago by
Ram
43k • written 6 days ago by
Raman
• 0
0
votes
7
replies
338
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
GenoMax
141k • written 6 days ago by
Patadu94
• 0
3
votes
3
replies
234
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 6 days ago by
GenoMax
141k • written 7 days ago by
Mariana
▴ 10
0
votes
1
reply
132
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 6 days ago by
ATpoint
82k • written 6 days ago by
enanoide
• 0
0
votes
0
replies
89
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
6 days ago by
manaswwm
▴ 510
3
votes
3
replies
723
views
KissDE and batch effect
kissDE
kissplice
6 days ago by
david.b.rombaut
▴ 10
0
votes
0
replies
80
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
6 days ago by
alifafiq1
• 0
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
4 days ago by
Kevin Blighe
87k
0
votes
0
replies
86
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
7 days ago by
feather-W
• 0
2
votes
4
replies
290
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
5 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
85
views
Annotating single cell data automatically
cell
annotation
single
7 days ago by
Gerard
• 0
0
votes
0
replies
87
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
7 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
133
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
7 days ago by
Ben_Ensembl
★ 2.4k
2
votes
4
replies
323
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
5 days ago by
HyperEvo
• 0
0
votes
1
reply
157
views
RNA-seq bacteria contamination
RNA-seq
updated 6 days ago by
GenoMax
141k • written 7 days ago by
sh
• 0
0
votes
2
replies
195
views
Result of running of p3_in.pl
primer3
updated 7 days ago by
GenoMax
141k • written 7 days ago by
nasri
• 0
0
votes
1
reply
138
views
FAM FILE
file
Fam
7 days ago by
Eleonora
• 0
0
votes
0
replies
75
views
Imputation advice
imputation
7 days ago by
kl
▴ 10
3
votes
5
replies
281
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 7 days ago by
GenoMax
141k • written 7 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
92
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
7 days ago by
Enrique
• 0
3
votes
5
replies
558
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
7 days ago by
n_navy
• 0
0
votes
0
replies
75
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
7 days ago by
sativus
▴ 20
6
votes
3
replies
187
views
Interpretting IGV output
IGV
updated 7 days ago by
Carlo Yague
8.7k • written 7 days ago by
analyst
▴ 30
0
votes
1
reply
178
views
homology modelling using swiss model
homology-modeling
swiss-model
updated 7 days ago by
colindaven
6.4k • written 7 days ago by
Ayush
• 0
0
votes
0
replies
82
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
7 days ago by
Biostars2200
• 0
1
vote
5
replies
354
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
5 days ago by
anasjamshed
▴ 120
0
votes
0
replies
134
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 7 days ago by
Carlo Yague
8.7k • written 7 days ago by
Atul K.
• 0
3
votes
2
replies
280
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
6 days ago by
kristiewyleung
• 0
2
votes
5
replies
461
views
Marking duplicates using UMIs
Deduplication
UMI
updated 7 days ago by
i.sudbery
19k • written 8 days ago by
Lipika
• 0
0
votes
0
replies
141
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 7 days ago by
Ram
43k • written 8 days ago by
sainavyav22
• 0
0
votes
0
replies
142
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
8 days ago by
rthapa
▴ 90
0
votes
0
replies
136
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
8 days ago by
Mamatha Y S
• 0
0
votes
0
replies
133
views
News:
upcoming online statistical courses
Statistics
R
Data-Analysis
updated 7 days ago by
Ram
43k • written 8 days ago by
carlopecoraro2
★ 2.5k
0
votes
4
replies
537
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 8 days ago by
ATpoint
82k • written 9 days ago by
rheab1230
▴ 140
0
votes
2
replies
275
views
bam merging for archaic samples
samtools
bam
updated 7 days ago by
Ram
43k • written 8 days ago by
Matteo Ungaro
▴ 100
7
votes
6
replies
497
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
7 days ago by
analyst
▴ 30
1
vote
1
reply
267
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 9 days ago by
Gordon Smyth
★ 7.0k • written 9 days ago by
Bioinformatician
• 0
1
vote
0
replies
544
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
9 days ago by
mathavanbioinfo
▴ 90
1
vote
1
reply
303
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 9 days ago by
Ram
43k • written 9 days ago by
Nina
• 0
2
votes
5
replies
540
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 8 days ago by
Mensur Dlakic
★ 27k • written 9 days ago by
Giorgio
• 0
2
votes
1
reply
294
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 9 days ago by
GenoMax
141k • written 9 days ago by
rebecca.calvo
• 0
0
votes
0
replies
216
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
8 days ago by
abhishekghadge
• 0
2
votes
5
replies
703
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 8 days ago by
Jesse
▴ 740 • written 9 days ago by
Ann
★ 2.4k
0
votes
0
replies
191
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 9 days ago by
Ram
43k • written 9 days ago by
mja
• 0
0
votes
0
replies
191
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
9 days ago by
Nitin
• 0
1
vote
5
replies
574
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 9 days ago by
GenoMax
141k • written 9 days ago by
Luka
• 0
0
votes
0
replies
185
views
Chemical structure validation
structure
cap
validation
metabolite
9 days ago by
Rodolfo Adrián
• 0
1,000 results • Page
4 of 20
Recent Votes
A: vcf calculation of allele counts and allele number
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
which tool/software/package should I use to preprocess the rosetta-merck microarray platform raw data?
Answer: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: What does it mean single base resolution in sequencing?
by
GenoMax
141k
>You known, 90% + genomic region is transcripted. So, total RNA-seq theoretically covers most genome region. Perhaps but not all of that …
Answer: Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mous
by
trausch
★ 1.9k
For [delly][1], we usually augment the mouse reference genome with the additional sequence, then remap and then look in the delly output fo…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
Thats very intersting! What are the features in your classifier?
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
hagl
▴ 10
Thank you very much for the response. Following your recommendation in pursuing option one by selecting highest expressions and subsequent …
Answer: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
I think it would be pertinent to use DESEq2 to perform two comparisons: the first one between the control group and condition 1, and the se…
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
Lluís R.
★ 1.2k
Many thanks for the helpful comment. Indeed, I read some of them, but I was not fully convinced and I missed the link FAQ of DESeq2. The re…
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
ATpoint
82k
Keeping data together is most powerful and most convenient as you have a single analysis object and a single count matrix. I would always d…
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
Assuming you have network access and the md5sum is registered with the EBI's reference server, yes - it'll be downloaded and cached locally.
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I followed your advice and it seems that I'm getting results comparable to what I was getting before. Upon checking with `wc -l` on the ori…
Comment: Finding batch and outlayers
by
christopher medway
▴ 450
You could perform an ANOVA to test if there is a significant association between batch number and a given Principal Component
Comment: ChIP-seq datasets: input samples omitted?
by
i.sudbery
19k
Fascinating! We also use inputs when doing metagene to protect against those situations where regions up or downstream of our metagene al…
Answer: How to solve DESeq2 Error in checkFullRank(modelMatrix)?
by
i.sudbery
19k
See the section on non full rank design matrices in the DESeq2 manual. In this case your problem is that healthy and 0dpi samples are e…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
Can you clarify what you mean by "100% of reads pass cutadapt, even though 70% of reads contain adapters and get trimmed. " did you set a m…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
I don't follow your argument for distinguishing between genomic contamination and freud. A data set being bad in terms of genomic contamin…
Comment: What does it mean single base resolution in sequencing?
by
jinyu
▴ 10
Thank you for your detail and great explanation. I do need more time to understand these. And there is still something compuzzling me. For …
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