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Limit : this week
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125 results • Page
2 of 3
Sort: replies
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Views
Votes
Replies
0
votes
2
replies
770
views
Error in mvnX when running processSamples.R of OncoCNV
variant-calling
oncocnv
cnv
updated 19 hours ago by
Ram
39k • written 3.5 years ago by
mwarrier
• 0
1
vote
2
replies
209
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
5 days ago by
rheab1230
▴ 140
0
votes
2
replies
175
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 6 days ago by
rpolicastro
12k • written 6 days ago by
Pac314
▴ 10
1
vote
2
replies
48
views
Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
RNA-evidence
genome
prediction
masking
52 minutes ago by
Ayish
• 0
0
votes
2
replies
223
views
Diff Bind Questions
DiffBind
CHiP-Seq
updated 17 hours ago by
Ram
39k • written 1 day ago by
B.N.
• 0
1
vote
2
replies
521
views
How to mine plant-inducible promoter (PIP) box from Xanthomonas genus genome?
assembly
gene
genome
next-gen
updated 1 day ago by
Ram
39k • written 3.6 years ago by
Kumar
▴ 100
0
votes
2
replies
238
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
1 day ago by
demoraesdiogo2017
▴ 90
1
vote
2
replies
227
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 4 days ago by
thadjudkins2
• 0 • written 5 days ago by
herh
• 0
0
votes
1
reply
749
views
plasmid spades R1/R2 files?
plasmid
sequencing
updated 4 days ago by
Ram
39k • written 3.7 years ago by
sarah.goldstein
• 0
1
vote
1
reply
599
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 5 days ago by
GenoMax
129k • written 5 days ago by
Mohd
▴ 20
0
votes
1
reply
168
views
CHiP-Seq Questions
DiffBind
CHiP-Seq
updated 1 day ago by
jared.andrews07
★ 14k • written 1 day ago by
B.N.
• 0
0
votes
1
reply
686
views
Small demo bioinformatics workflows which don't require reference data?
workflow
pipeline
updated 4 days ago by
Ram
39k • written 3.7 years ago by
steve
★ 3.3k
0
votes
1
reply
69
views
What is the possibility of Depth (DP) being higher than the coverage
GATK
DP
Coverage
Depth
HaplotypeCaller
updated 5 hours ago by
seidel
11k • written 6 hours ago by
dare_devil
★ 3.1k
1
vote
1
reply
129
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 6 days ago by
GenoMax
129k • written 6 days ago by
hashim.rana11
▴ 20
2
votes
1
reply
1.8k
views
How do I apply a patch to hg38?
reference
human
freeze
hg38
patch
updated 5 days ago by
Jeremy Leipzig
21k • written 5.6 years ago by
imperialcommando117
• 0
0
votes
1
reply
126
views
phage genome submission in ncbi genebank
phage
table2asn
ncbi
updated 15 hours ago by
acvill
▴ 290 • written 22 hours ago by
tahsinkhan570
• 0
0
votes
1
reply
381
views
How to quantification proteomics data
proteomics
updated 1 day ago by
eqoa45
• 0 • written 19 months ago by
LeeLee
▴ 10
0
votes
1
reply
258
views
Comparing loci across catalogs
Stacks
reference
alignment
RADseq
adegenet
updated 4 days ago by
rycro_c
• 0 • written 13 months ago by
Austin
• 0
0
votes
1
reply
159
views
Where to get the molecular subtype information of STAD sample in TCGA
TCGA
database
updated 2 days ago by
Hamid Ghaedi
2.9k • written 3 days ago by
younglin113
▴ 50
1
vote
1
reply
1.6k
views
Bioinformatics tools for Plasmid detection
short-read
plasmid
updated 5 days ago by
Ram
39k • written 3.9 years ago by
El Niño
▴ 10
1
vote
1
reply
3.1k
views
Problem with PGDSpider v 2.1.0.2
alignment
updated 6 days ago by
sackettl
▴ 20 • written 7.0 years ago by
maria.segovia.ramirez
▴ 10
0
votes
1
reply
94
views
CIBERSORT Error: File not found
CIBERSORT
updated 4 hours ago by
ATpoint
72k • written 14 hours ago by
jcara514
• 0
0
votes
1
reply
1.2k
views
Best tool for bacterial genomic island prediction?
genome
genomic-island
updated 6 days ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
0
votes
1
reply
185
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
updated 4 days ago by
raphael.B
▴ 360 • written 5 days ago by
sonsunjirachote
• 0
0
votes
1
reply
158
views
Information on sequin RNA spike in standards
Sequin
Spike-in
RNA-seq
updated 3 hours ago by
ATpoint
72k • written 1 day ago by
akainth
▴ 10
0
votes
1
reply
165
views
Merge different vcf files
vcf
updated 4 days ago by
Ram
39k • written 5 days ago by
caique.manochio
• 0
0
votes
1
reply
813
views
Filtering for homozygous reference alleles
SNP
sequence
genome
updated 4 days ago by
Ram
39k • written 3.7 years ago by
AGE
▴ 30
0
votes
1
reply
873
views
Masters in Bioinformatics
masters
structural-bioinformatics
assistantship
updated 5 days ago by
Ram
39k • written 3.9 years ago by
Manvitha Reddy
▴ 10
0
votes
1
reply
145
views
Pairwise Alignment
Pairwise-Alignment
updated 1 day ago by
Ram
39k • written 2 days ago by
Fatemeh
• 0
0
votes
0
replies
116
views
Convert tree into bifurcation table
Tree
Newick
ASR
Mutation
5 days ago by
Alexandre
• 0
1
vote
0
replies
109
views
How to predict gene amplification from RNAseq and ATACseq data?
amplification
ATAC
1 day ago by
Dan
▴ 120
0
votes
0
replies
86
views
How to extract only neutral markers from low-coverage whole genome sequencing?
low-coverage
whole-genome-sequencing
updated 1 day ago by
Ram
39k • written 1 day ago by
beausoleilmo
▴ 530
0
votes
0
replies
536
views
Online courses/studies bioinformatics
online-study
learning
updated 4 days ago by
Ram
39k • written 3.8 years ago by
MAR
• 0
0
votes
0
replies
124
views
cnetplot enrichment graph to cytoscape
clusterprofiler
cnetplot
enrichplot
5 days ago by
Omics data mining
▴ 220
0
votes
0
replies
100
views
What statistical test should I use to analyse my two set of transcriptomique data?
transcriptome
1 day ago by
F.Bedjou
▴ 10
1
vote
0
replies
154
views
Bayesian network for biological data using bnlearn
bnlearn
RNA-seq
bayesian-network
updated 4 days ago by
Ram
39k • written 4 days ago by
priyankamehta.1811
▴ 10
1
vote
0
replies
97
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
5 days ago by
Jonathan Lefebre
▴ 70
0
votes
0
replies
7
views
ERROR: LoadError: UndefVarError: `composition` not defined ?
Protpram
30 minutes ago by
Sapphire
• 0
0
votes
0
replies
588
views
Taxonomy from Pfam database
taxonomy
pfam
updated 17 hours ago by
Ram
39k • written 3.5 years ago by
shibl_a
▴ 20
0
votes
0
replies
148
views
jellyfish options
kmer
jellyfish
4 days ago by
Tele
• 0
0
votes
0
replies
111
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
6 days ago by
Maddie
• 0
0
votes
0
replies
159
views
busco id description
OrthoDB
BUSCO
updated 4 days ago by
Ram
39k • written 4 days ago by
angelina
• 0
0
votes
0
replies
19
views
Complex Phylogenetic Tree Annotation
annotation
tree
protein
phylogenetic
1 hour ago by
Aanushka
• 0
0
votes
0
replies
80
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 5 days ago by
Ram
39k • written 6 days ago by
Rishabh Jha
• 0
0
votes
0
replies
106
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
6 days ago by
mbk0asis
▴ 670
0
votes
0
replies
172
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential
visualization
RNASeq
analysis
expression
enrichment
4 days ago by
Mark
• 0
0
votes
0
replies
87
views
Why sone miRNAs are not present in TCGA data
TCGA
miRNA
RNA-seq
2 days ago by
nicolo.gualandi
• 0
0
votes
0
replies
368
views
How to compile Java files in bash?
Bash
Java
updated 19 hours ago by
Ram
39k • written 19 months ago by
ezraamustafa3
• 0
0
votes
0
replies
110
views
Error occured at the PHG imputation step: allele in genotype not in the variant context
PHG
Imputation
PracticalHaplotypeGraph
Haplotype
1 day ago by
xeod21
• 0
0
votes
0
replies
606
views
Pan-genome Bioinformatics Workshops?
pan-genome
workshop
updated 1 day ago by
Ram
39k • written 3.7 years ago by
cassondranewman
• 0
125 results • Page
2 of 3
Recent Votes
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
Answer: Alignment of case vs. control from different origin
Comment: Alignment of case vs. control from different origin
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Recent Replies
Comment: Differential protein expression analysis
by
Ribo
▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
No, your code isn't correct. You are testing an intercept equal to zero instead of testing for a logFC. I wonder what comparison you were t…
Answer: Extract sequences from a fastq file by a list of IDs
by
GenoMax
129k
Using `filterbyname.sh` from [**BBMap suite**][1]: You need to include the `/1` in the header in your list file (here I am using the `nam…
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
Yeah, I added the design matrix. `design <- model.matrix(~0+group)`. These are raw counts.
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Ayish
• 0
Thank you for reply. I have Illumina paired-end reads. Would it be fine if I use hard-masking for STAR and soft-masked genome for BRAKER2? …
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Darked89
4.4k
Soft masking the genome (unless something changed) not make any difference for STAR. Depending on how your RNA-Seq is done (Illumina? paire…
Answer: How to handle NaN in emmax Kinship matrix?
by
Thu
• 0
Hi! Thanks for sharing your solution! It works! :)
Comment: Gene prediction software
by
Darked89
4.4k
Looks like there are five Clarias genomes: * https://www.ncbi.nlm.nih.gov/genome/?term=txid13012[Organism:exp] The most complete seems t…
Comment: Alignment of case vs. control from different origin
by
sativus
▴ 10
Again, thank you so much for these very clearly explained summaries. After reading some articles on the matter, i feel i have a much better…
Answer: Extract sequences from a fastq file by a list of IDs
by
colindaven
4.9k
Some people I know have used filter-fastq successfully: https://github.com/Floor-Lab/filter-fastq
Comment: Extract sequences from a fastq file by a list of IDs
by
Pierre Lindenbaum
154k
> but none of them work for me https://meta.stackexchange.com/questions/147616/
Comment: Extract sequences from a fastq file by a list of IDs
by
Pierre Lindenbaum
154k
https://meta.stackexchange.com/questions/147616/
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
I have tried this one before but the output file is empty
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
I have tried all of them but none of them work for me
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