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1,000 results • Page
3 of 20
Sort: Votes
Rank
Views
Votes
Replies
10
votes
7
replies
1.2k
views
Better DE analytic tools
RNA-Seq
DE tools
Bayesian empirical approach
6.0 years ago by
mhyunjunkang
▴ 110
10
votes
5
replies
7.3k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing
Assembly
alignment
updated 21 months ago by
Ram
44k • written 8.7 years ago by
seta
★ 1.9k
10
votes
2
replies
610
views
any script that can do this task
shell-script
updated 2.2 years ago by
Ram
44k • written 2.2 years ago by
Confused_human
▴ 20
10
votes
14
replies
5.0k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 11 months ago by
Ram
44k • written 4.3 years ago by
gable_works
▴ 50
10
votes
10
replies
3.9k
views
Parameter optimization STAR
RNA-Seq
6.3 years ago by
XBria
▴ 90
10
votes
11
replies
9.2k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 23 months ago by
Ram
44k • written 9.2 years ago by
SheelS
▴ 40
10
votes
8
replies
2.3k
views
Blast scores...two annotations for the same piece of sequence
alignment
updated 23 months ago by
Ram
44k • written 9.1 years ago by
friasoler
▴ 50
10
votes
6
replies
8.5k
views
Any idea how to solve this error in fgsea - "Error in if (any(simpleFgseaRes$modeFraction < 10)) { : missing value where TRUE/FALSE needed"?
fgsea
updated 2.9 years ago by
alserg
▴ 930 • written 2.9 years ago by
gabrielbaldanzi
▴ 10
10
votes
25
replies
3.6k
views
The interpretation of PCA
DESeq2
R
PCA
updated 5.8 years ago by
Biostar
20 • written 5.9 years ago by
Za
▴ 140
10
votes
15
replies
6.3k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 14 months ago by
Ram
44k • written 5.6 years ago by
marongiu.luigi
▴ 710
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database
analysis
ontology
pathway
updated 11 months ago by
Ram
44k • written 8.1 years ago by
Pranavathiyani G
▴ 330
10
votes
10
replies
2.1k
views
Minor allele frequency
GWAS
SNPs
Alleles
updated 5.5 years ago by
Biostar
20 • written 7.5 years ago by
alessandrotestori7
▴ 420
10
votes
5
replies
5.6k
views
Intron Retention And Alternative 5'3' Splice Site Identification
updated 10.3 years ago by
Biostar
20 • written 13.1 years ago by
Arun
2.4k
10
votes
6
replies
2.9k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 14 months ago by
Ram
44k • written 9.0 years ago by
lait
▴ 180
9
votes
13
replies
3.4k
views
Python Script to map reads to reference sequence
sequence
python
mapping
script
reference sequence
5.1 years ago by
Fid_o
▴ 40
9
votes
5
replies
1.2k
views
how to retrieve all proteins related to cancer
proteins
8.0 years ago by
Learner
▴ 280
9
votes
7
replies
3.3k
views
Aligning Miseq With Deletions >10 Bases
alignment
miseq
next-gen
updated 10.8 years ago by
Biostar
20 • written 11.4 years ago by
Leszek
4.2k
9
votes
13
replies
1.7k
views
SNP's and Gene?
SNP
gene
4.6 years ago by
imgapgenomika
▴ 10
9
votes
16
replies
1.5k
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 3.8 years ago by
lieven.sterck
15k • written 3.8 years ago by
schlogl
▴ 160
9
votes
7
replies
5.4k
views
How to combine a different sources of pathway database (KEGG, BioCarta) for Pathway analysis.
Pathway
enrichment analysis
GWAS
pathway analysis
7.9 years ago by
kmsh410
▴ 40
9
votes
10
replies
2.9k
views
About GATK4 Mutect2 runtime (Whole Exome seq)
GATK
Whole Exome Sequencing
Mutect2
3.3 years ago by
kwanghoon
▴ 20
9
votes
5
replies
3.9k
views
What's the interpretation behind Pathway enrichment analysis
networks
pathway enrichment analysis
gene
updated 6.7 years ago by
Biostar
20 • written 6.9 years ago by
Chaimaa
▴ 260
9
votes
11
replies
6.6k
views
microRNA Illumina Sequencing - Very low alignment rate
sequencing
Assembly
RNA-Seq
updated 2.3 years ago by
Ram
44k • written 9.8 years ago by
wynstep
▴ 90
9
votes
16
replies
2.0k
views
feature extraction from SNPs in R
R
gene
sequence
SNP
5.5 years ago by
bioinfo456
▴ 150
9
votes
19
replies
2.4k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
4.3 years ago by
schlogl
▴ 160
9
votes
6
replies
3.5k
views
SOAPaligner 2.21 - does it replace all Ns by Gs in reads?
Soapaligner
alignment
updated 2.6 years ago by
Ram
44k • written 10.0 years ago by
Philipp Bayer
8.5k
9
votes
27
replies
7.7k
views
How do I use Glimmer 3.02?
sequencing
updated 5.3 years ago by
ojelizodun
• 0 • written 6.2 years ago by
nattzy94
▴ 50
9
votes
13
replies
2.0k
views
Archeological DNA sample - how to analyze
unmapped
paleogenomics
archeogenomics
Assembly
2.3 years ago by
Aruna
▴ 30
9
votes
9
replies
1.6k
views
Convert mouse amino acid location to genomic location
genome
gene
4.9 years ago by
L. A. Liggett
▴ 120
9
votes
14
replies
3.1k
views
vcf to xls wrong columns
vcf
7.8 years ago by
cristina_sabiers
▴ 110
9
votes
6
replies
1.4k
views
Genotype meaning
genotype
BL21
2.9 years ago by
A_heath
▴ 160
9
votes
4
replies
1.3k
views
Is there any method to run tophat ?
RNA-Seq
updated 5.7 years ago by
Biostar
20 • written 5.8 years ago by
Chan
• 0
9
votes
9
replies
4.7k
views
ATAC-seq TSS profile plot interpretation
ATAC-seq
TSS
V-plot
4.5 years ago by
nanoide
▴ 120
9
votes
2
replies
5.3k
views
Biopython Import Error
biopython
updated 12.0 years ago by
Michael Kuhn
5.0k • written 12.0 years ago by
angeles.sepulvedap
• 0
9
votes
7
replies
3.8k
views
7 follow
Are 2 replicates per sample sufficient for RNA-seq data analysis?
RNA-Seq
R
Ngs
6.3 years ago by
Arindam Ghosh
▴ 510
9
votes
7
replies
2.5k
views
Merging BWT indices for BWA
BWA
BWT
read aligner
merge
5.6 years ago by
rgc255
▴ 60
9
votes
11
replies
8.2k
views
8 follow
Extremely low mapping rates with bowtie2
alignment
next-gen
updated 6.6 years ago by
Biostar
20 • written 6.6 years ago by
Sachin
▴ 10
9
votes
12
replies
7.4k
views
How to align reads on reference using python?
genome
sequence
gene
sequencing
updated 5.4 years ago by
WouterDeCoster
47k • written 5.4 years ago by
doramora
▴ 10
9
votes
4
replies
2.1k
views
[Code] Converte fasta/fa files to fastq
perl
fastq
sed
fasta
updated 21 months ago by
Ram
44k • written 8.5 years ago by
Shicheng Guo
★ 9.4k
9
votes
7
replies
2.2k
views
Sorting BLAST output files together?
blast
8.1 years ago by
zgayk
▴ 90
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 11 months ago by
Ram
44k • written 5.7 years ago by
Shahzad
▴ 30
9
votes
10
replies
2.3k
views
[solved] Convert fold changes of multiple transcripts of a given gene to a single value characterising this gene
RNA-Seq
7.7 years ago by
biostart
▴ 370
9
votes
8
replies
1.7k
views
Union of unaligned fastq reads
RNA-Seq
6.9 years ago by
Jeffin Rockey
★ 1.3k
9
votes
12
replies
1.5k
views
Copy number variations analysis
R
CNV
updated 4.5 years ago by
zx8754
11k • written 4.5 years ago by
rprog008
▴ 70
9
votes
7
replies
1.2k
views
ChIP-seq; investigate binding within region of tRNA genes
tRNA
ChIP
nf-core
ChIP-seq
updated 2.0 years ago by
Ram
44k • written 2.1 years ago by
2138493o
▴ 20
9
votes
15
replies
1.4k
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
5 months ago by
analyst
▴ 50
9
votes
11
replies
1.5k
views
6 follow
Split up excel cell into multiple records
excel
byonic
6.9 years ago by
rshipman
▴ 30
9
votes
13
replies
2.5k
views
Reannotating a gene: Identifying translation and transcription start sites
RNA-Seq
genome
gene
7.4 years ago by
rh5118
▴ 40
9
votes
4
replies
1.7k
views
On which branch in bioinformatics should a cancer researcher focus on ?
cancer
updated 13 months ago by
Ram
44k • written 7.8 years ago by
Bilal
▴ 60
9
votes
7
replies
5.6k
views
fisher test with multiple samples
statistics
updated 2.5 years ago by
Ram
44k • written 9.8 years ago by
juncheng
▴ 220
1,000 results • Page
3 of 20
Recent Votes
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Comment: Trimming tool
Answer: Trimming tool
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
Comment: Practical Haplotype Graph v2 not finding correct paths
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Recent Replies
Answer: z-score of gene set
by
Matthias Zepper
4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set
by
bk11
★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
by
DBScan
▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
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
▴ 220
The timing for your question is excellent. The fix was released yesterday.
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