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1,000 results • Page
2 of 20
Sort: Views
Rank
Views
Votes
Replies
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 15 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
5
votes
35
replies
3.8k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 10 months ago by
Jordan M Eizenga
▴ 460 • written 11 months ago by
anivlete
• 0
2
votes
4
replies
3.8k
views
Converting different annotation file formats (GTF/GFF/BED) to each other
rna-seq
next-gen
updated 7 months ago by
alejandrogzi
▴ 120 • written 6.7 years ago by
Javad
▴ 150
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database
analysis
ontology
pathway
updated 11 months ago by
Ram
43k • written 8.1 years ago by
Pranavathiyani G
▴ 330
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 5 weeks ago by
Ram
43k • written 6.6 years ago by
firestar
★ 1.6k
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 7 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
1
vote
2
replies
3.6k
views
rna-seq analysis with Salmon - how to Import and summarize using tximport
RNA-Seq
salmon
tximport
updated 7 months ago by
camillab.
▴ 160 • written 4.7 years ago by
woojoy14
▴ 10
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 8 weeks ago by
Ram
43k • written 5.6 years ago by
c.clarido
▴ 110
0
votes
2
replies
3.5k
views
dN/dS ratio from .vcf file
synonmous
non-synomous
mutation
updated 7 months ago by
rohitsatyam102
▴ 870 • written 5.5 years ago by
shubhra.bhattacharya
▴ 140
3
votes
4
replies
3.5k
views
Switch ref/alt alleles vcf file
SNP
vcf
sequencing
updated 4 months ago by
jvt
• 0 • written 4.5 years ago by
mdstep
▴ 20
4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan
SNP
updated 10 months ago by
Ram
43k • written 9.6 years ago by
zhaojianli198322
• 0
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 4 weeks ago by
Ram
43k • written 7.2 years ago by
dyollluap
▴ 310
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 4 weeks ago by
Ram
43k • written 7.1 years ago by
tud55122
▴ 20
2
votes
10
replies
3.5k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 4 weeks ago by
Ram
43k • written 7.5 years ago by
linda
• 0
1
vote
1
reply
3.4k
views
Problem with PGDSpider v 2.1.0.2
alignment
updated 11 months ago by
sackettl
▴ 20 • written 7.9 years ago by
maria.segovia.ramirez
▴ 10
0
votes
4
replies
3.4k
views
Polyploidy found, and not supported by vcftools
SNP
updated 11 months ago by
Ram
43k • written 5.3 years ago by
sambioinfo2018
▴ 20
1
vote
2
replies
3.4k
views
How to convert FASTA to NEXUS in Python
fasta
biopython
nexus
updated 10 months ago by
Ram
43k • written 3.8 years ago by
adrian18_07
▴ 10
20
votes
17
replies
3.4k
views
How to add "transcript" feature to a gtf file?
gtf
updated 10 months ago by
1769mkc
★ 1.2k • written 3.3 years ago by
pomodoro_sinensis
▴ 110
1
vote
14
replies
3.4k
views
How to convert Haplotypes file to PLINK format data
R
plink
updated 12 months ago by
Ram
43k • written 6.0 years ago by
bha
▴ 80
2
votes
12
replies
3.4k
views
WCGNA installation help
R
WGCNA
updated 3 months ago by
Ram
43k • written 5.0 years ago by
prekrish
• 0
1
vote
9
replies
3.4k
views
build databses for genome using snpEff
annotation
SNP
snpEff
updated 9 months ago by
nehakhilwani18
• 0 • written 5.8 years ago by
StudentBio
• 0
2
votes
5
replies
3.3k
views
How to output colored alignment from clustal omega stand alone tool?
Clustal Omega
Colored alignment
updated 9 months ago by
Joe
21k • written 4.8 years ago by
MB
▴ 50
1
vote
6
replies
3.3k
views
Filter VCF file
snp
next-gen
updated 10 months ago by
Ram
43k • written 7.9 years ago by
sukesh1411
▴ 30
0
votes
1
reply
3.3k
views
Cutadapt 1.9.1 error
cutadapt
next-gen
updated 11 months ago by
Ram
43k • written 8.2 years ago by
vishweshwaransridhar
▴ 10
3
votes
6
replies
3.3k
views
samtools sort not working when using multiple threads
samtools
bam
updated 11 months ago by
Ram
43k • written 2.3 years ago by
bio_elle
▴ 10
3
votes
7
replies
3.3k
views
vcf filter for FORMAT argument (DP/GQ/GQX > 30) multiple (380) vcf file
vcffilter
vcftools
sequencing
updated 10 months ago by
Ram
43k • written 4.2 years ago by
IndyDNA
▴ 10
2
votes
10
replies
3.2k
views
6 follow
Split plink files by a number of SNPs
GWAS
SNP
plink
updated 7 months ago by
Raygozak
★ 1.4k • written 5.9 years ago by
kakukeshi
▴ 80
3
votes
5
replies
3.2k
views
GO annotation for rice in an R package
annotation
R
updated 3 months ago by
prity6459
• 0 • written 7.5 years ago by
djyjin
▴ 10
0
votes
1
reply
3.2k
views
How to convert g.vcf to .vcf file
vcf
sequence
genome
alignment
updated 11 months ago by
Ram
43k • written 5.1 years ago by
Sakhaa
• 0
5
votes
7
replies
3.2k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP
genome
sequence
updated 7 months ago by
Istvan Albert
100k • written 5.9 years ago by
chris.bird
▴ 10
0
votes
1
reply
3.2k
views
PSMC plot (Effective population size)
next-gen
updated 8 months ago by
1601693223
• 0 • written 8.5 years ago by
vicky
▴ 30
2
votes
6
replies
3.2k
views
hisat2 :Killed (ERR): hisat2-align exited with value 137
RNA-seq
alignment
hisat2
updated 8 months ago by
Ram
43k • written 2.4 years ago by
iamsmor
• 0
1
vote
7
replies
3.1k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT
TF-footprinting
ATAC-seq
updated 11 months ago by
Ram
43k • written 5.5 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
10
replies
3.1k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 12 months ago by
Ram
43k • written 5.2 years ago by
Kumar
▴ 120
3
votes
12
replies
3.1k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 11 months ago by
Pegasus
▴ 100 • written 4.6 years ago by
mnazir
▴ 10
3
votes
6
replies
3.1k
views
Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
gatk
variant calling
sureselect
updated 10 months ago by
LeandroF.
• 0 • written 4.3 years ago by
curious
▴ 750
1
vote
5
replies
3.1k
views
Problem in running NOISeq-sim
NOISeq
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.8 years ago by
jaspreetk.dhanjal
▴ 20
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 4 weeks ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
0
votes
2
replies
3.1k
views
How to convert gbk file to roary tool acceptable gff3 format?
linux
bash
python
perl
updated 11 months ago by
Ram
43k • written 3.7 years ago by
Kumar
▴ 120
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 4 weeks ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
6
votes
9
replies
3.0k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool
Cellranger
NCBI
updated 11 months ago by
Ram
43k • written 2.4 years ago by
aimanbarki
▴ 20
0
votes
1
reply
3.0k
views
RNA-seq compare FPKM's or fold change of different organisms
gene-expression
FPKM
RNA-seq
fold-change
updated 8 months ago by
Ram
43k • written 6.8 years ago by
jehu
▴ 30
1
vote
4
replies
2.9k
views
DBD::mysql::st execute failed: The table 'InplgOrthoInplg
orthomcl
ortho
ubuntu
mysql
updated 12 months ago by
Ram
43k • written 5.9 years ago by
wocana
▴ 20
0
votes
7
replies
2.9k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr
fold-change
updated 8 months ago by
Ram
43k • written 5.9 years ago by
AP
▴ 80
2
votes
3
replies
2.9k
views
Merge really large amount of Seurat objects
Seurat
10 months ago by
Andy
▴ 120
0
votes
0
replies
2.9k
views
TCGA RNAseqVer2 batch effects
TCGA
RNA-Seq
batch-effect
updated 4 weeks ago by
Ram
43k • written 8.6 years ago by
annadv
• 0
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 22 days ago by
dimpleadiwal050896
• 0 • written 5.0 years ago by
ggman
▴ 90
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 4 weeks ago by
Ram
43k • written 7.1 years ago by
endikavarela
• 0
0
votes
3
replies
2.8k
views
Generate GTF/GFF file (coordinates) from a FASTA annotated file.
Assembly
genome
updated 11 months ago by
Ram
43k • written 4.7 years ago by
marquezg48
• 0
3
votes
3
replies
2.8k
views
WGCNA Labeled Heatmap
heatmap
wgcna
updated 7 months ago by
Ram
43k • written 2.7 years ago by
Anand
▴ 40
1,000 results • Page
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Recent Votes
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Comment: What marks a De-Novo Genome assembly as FAILED?
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Recent Replies
Answer: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results
by
Bjorn
• 0
Thank you!
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file
by
pirku
• 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice
by
GenoMax
142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
Answer: Running STRUCTURE from command line
by
Arthur
• 0
If it cans help, I got the same error message : There were errors in the input file (listed above). According to "mainparams" the inp…
Comment: CreateSeuratObject taking very long
by
Nitin Narwade
★ 1.6k
I am not sure whether it will speedup the conversion but you can give it a try. convert your dataframe into a sparse matrix before creatin…
Comment: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 210
The timing for your question is excellent. The fix was released yesterday.
Comment: vcf phasing
by
WouterDeCoster
47k
> I observed that it doesn't phase genotypes labeled as 0/0 How could such a genotype even be phased?
Comment: Super ehancers
by
Oburah
• 0
Well-noted however just wondering what you me by GFF being shorter. Thank you![See the screeshot snap of the gff file][1] [1]: /media/i…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
I know illumina will only give me high-quality contigs. the samples which are to be sequenced with Long_Short read sequence will be used as…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Hi, Thank you for a detailed responce. Let me add some more informations. Long-Read is ~75X coverage. Short-Read is ~100X coverage. **For…
Comment: Pruning Phylogenetic Trees and Bootstrap Values
by
Klaus S
▴ 160
The best is to prune the tree and also the bootstrap trees and afterwards re-assign the bootstrap values to the tree. The bootstrap values …
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