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1,000 results • Page
2 of 20
Sort: Views
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Views
Votes
Replies
0
votes
3
replies
13k
views
edgeR: likelihood ratio test or quasi-likelihood F-test?
R
rna-seq
next-gen
7.0 years ago by
moxu
▴ 510
4
votes
9
replies
13k
views
Seqtk subseq: structure of file name.lst
sequence
next-gen
updated 6.0 years ago by
Ram
43k • written 6.0 years ago by
ste.lu
▴ 80
2
votes
13
replies
12k
views
8 follow
(ERR): bowtie2-align exited with value 1
software error
RNA-Seq
updated 6.2 years ago by
basucsmcri
• 0 • written 7.2 years ago by
biostarsb
▴ 30
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
ncbi
nBLAST
linux
blast
updated 19 months ago by
Ram
43k • written 8.6 years ago by
Abdul Rafay Khan
★ 1.2k
41
votes
55
replies
12k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
8.1 years ago by
midox
▴ 290
0
votes
1
reply
12k
views
PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
plink
updated 7.7 years ago by
Biostar
20 • written 7.7 years ago by
rednalf
▴ 90
3
votes
8
replies
12k
views
6 follow
How do I go from UniProt ID to retrieving the gene name?
sequence
6.4 years ago by
a.rex
▴ 350
3
votes
2
replies
12k
views
ExAC PLI score calculation
DNA-Seq
7.2 years ago by
jonessara770
▴ 240
7
votes
9
replies
12k
views
Different alignment rates for Hisat2 and STAR, Hisat2 has lower alignment rate and STAR have many multi aligned reads
RNA-Seq
updated 6.6 years ago by
Satyajeet Khare
★ 1.6k • written 6.6 years ago by
SMILE
▴ 170
2
votes
13
replies
12k
views
MarkDuplicates memory issue
alignment
Picard
MarkDuplicates
8.3 years ago by
cacampbell
▴ 60
8
votes
5
replies
12k
views
samtools tview symbols
samtools
updated 17 months ago by
Ram
43k • written 8.8 years ago by
biolab
★ 1.4k
6
votes
7
replies
12k
views
bedtools intersect bed and vcf, coordinates problem
bedtools
bed
vcf
7.0 years ago by
abascalfederico
★ 1.2k
3
votes
4
replies
12k
views
basename: missing operand
snp
4.8 years ago by
evelyn
▴ 230
0
votes
3
replies
12k
views
Extracting Specific Columns from Multiple Files & Writing to File Python
python
file-handeling
7.9 years ago by
BioICoder
▴ 40
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 10 months ago by
Ram
43k • written 5.1 years ago by
Star
▴ 60
1
vote
2
replies
11k
views
Downloading BAM files GEO/SRA
bam
sra
geo
samtools
sratoolkit
7.7 years ago by
ilobelo
▴ 10
0
votes
4
replies
11k
views
Convert .gbf file to .gbk or .gff
gbk
gff
gbf
updated 15 months ago by
Ram
43k • written 8.9 years ago by
che.bellaj
• 0
4
votes
14
replies
11k
views
All the reads aligned using STAR have low mapping quality (0-3). What is happening?
mapping quality
STAR
BWA
alignment
7.7 years ago by
kirannbishwa01
★ 1.6k
2
votes
3
replies
11k
views
converting maf to vcf
Exome
maf2vcf
updated 15 months ago by
Ram
43k • written 8.9 years ago by
ashishchahl
• 0
3
votes
4
replies
11k
views
Zlib.Error: -3 While Decompressing: Invalid Distance To Far Back (By Using Macs For Chip-Seq Data)
error
12.6 years ago by
Lisanne
• 0
4
votes
7
replies
11k
views
Grab Coordinate Of Centromeres From Ucsc
ucsc
10.9 years ago by
jeansimon32
▴ 170
2
votes
8
replies
11k
views
Loading Custom Genome In Igv Is Not Displaying Genes, Names Match.
igv
gff
reference
contigs
12.2 years ago by
Nickengland
▴ 130
2
votes
4
replies
11k
views
Pymol-Generate Pymol Movie To Mpeg
pymol
updated 2.2 years ago by
Ram
43k • written 12.2 years ago by
Reyhaneh
▴ 530
5
votes
9
replies
11k
views
Error with samtools faidx...Different line length in sequence
samtools
faidx
updated 5.9 years ago by
Biostar
20 • written 6.1 years ago by
oars
▴ 200
6
votes
3
replies
11k
views
Sequence duplication levels-RNA Seq
RNA-Seq
updated 3.6 years ago by
joshua.theisen
▴ 30 • written 6.1 years ago by
makwana.kd
▴ 50
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 6 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
2
votes
0
replies
11k
views
How to plot UniFrac PCoA with 95% confidence Elipses in R
metagenomics
ordiellipse
vegan
R
phyloseq
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
c.v.oflynn
▴ 100
4
votes
11
replies
11k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF
snp
20 months ago by
prasundutta87
▴ 660
7
votes
8
replies
11k
views
Picard tools duplicate removal
RNA-Seq
picard-tools
6.5 years ago by
blur
▴ 280
3
votes
6
replies
10k
views
6 follow
How to calculate genetic correlation with R
R
updated 23 months ago by
ibomsolomon
• 0 • written 10.0 years ago by
Tohamy
▴ 80
2
votes
2
replies
10k
views
How to make clusters in heat map using ggplot2?
RNA-Seq
rna-seq
R
5.0 years ago by
John
▴ 270
3
votes
1
reply
10k
views
Negative P-Values
gene
genome
next-gen-sequencing
updated 20 months ago by
Ram
43k • written 8.6 years ago by
stevenlang123
▴ 210
3
votes
2
replies
10k
views
BWA-MEM Vs BWA-ALN
next-gen
genome
alignment
7.9 years ago by
SOHAIL
▴ 400
2
votes
8
replies
10k
views
Plotting different gene ontology categories in a barplot
HI
Gene ontology
R
updated 21 months ago by
zx8754
11k • written 3.2 years ago by
aradhana
• 0
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
trakhtenberg
▴ 160
0
votes
0
replies
10k
views
pheatmap row annotation and title font size questions
heatmap
pheatmap
updated 15 months ago by
Ram
43k • written 8.9 years ago by
neokao
• 0
5
votes
2
replies
10k
views
Turning Seq objects into strings
sequence
5.1 years ago by
schlogl
▴ 160
2
votes
1
reply
10k
views
Calculate Linkage Disequilibrium For Snps (Using R^2)
snp
linkage
10.8 years ago by
TitoPullo
▴ 180
1
vote
2
replies
10k
views
Converting MSTRG from stringtie with gene name
RNA-Seq
Stringtie
updated 6.3 years ago by
Biostar
20 • written 6.3 years ago by
fhassanz
▴ 20
2
votes
8
replies
10k
views
Size of typical genomic data
genomic
updated 13 months ago by
Ram
43k • written 5.9 years ago by
Nicolas Rosewick
10k
1
vote
7
replies
10k
views
How to find up-regulated and down-regulated genes after GEO2R analysis?
GEO
genes
up-regulated
down-regulated
GEO2R
6.1 years ago by
DanielC
▴ 170
7
votes
9
replies
10k
views
Samtools Index Segmentation Fault
samtools
index
10.1 years ago by
Noushin N
▴ 600
2
votes
4
replies
10k
views
num_threads with blastn in blast 2.6.0+
blast
5.3 years ago by
navela78
▴ 70
0
votes
1
reply
10k
views
Is it normal that nearly all of p-value is equal to 0.1 in PERMANOVA analysis
PERMANOVA
statistics
metagenomics
updated 3.3 years ago by
dqq102829
• 0 • written 4.3 years ago by
zhangdengwei
▴ 210
3
votes
3
replies
10k
views
bcftools mpileup output format
bcftools
mpileup
5.7 years ago by
tarek.mohamed
▴ 360
1
vote
5
replies
10k
views
What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With Gatk?
bed
agilent
gatk
updated 4.2 years ago by
Karma
▴ 310 • written 10.4 years ago by
newDNASeqer
▴ 760
0
votes
0
replies
10k
views
Map Between Uniprot Accesion And Gene.Symbol Using R Or/And Mysql
r
bioconductor
mysql
10.3 years ago by
jfertaj
▴ 110
3
votes
4
replies
10k
views
Aligning RNA seq data to genome or transcriptome
RNA-Seq
ngs
transcriptome
genome
updated 6.6 years ago by
Ram
43k • written 6.6 years ago by
KVC_bioinfo
▴ 590
1
vote
1
reply
10k
views
Raxml bootstrap support values
figtree
raxml
bootstrap
updated 2.6 years ago by
Ram
43k • written 9.9 years ago by
JackBel
• 0
2
votes
16
replies
10k
views
Tophat with Bowtie2 long index
tophat
bowtie
updated 2.3 years ago by
Ram
43k • written 9.8 years ago by
BDK_compbio
▴ 140
1,000 results • Page
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Recent Votes
Comment: Correlation for ATAC-Seq and Chip-Seq
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Comment: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
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Recent Replies
Comment: Heatmap and rna-seq
by
Basti
★ 2.0k
This forum is not dedicated to this type of request, there are many online tutorials for creating heatmaps accessible with simple internet …
Answer: python file for coding potential calculator
by
atharvakarkare14
▴ 10
Download the CPC2 tool supported by python 3 from here [https://github.com/gao-lab/CPC2_standalone/releases/tag/v1.0.1][1]. Then follow …
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
let me know the scope and scale of the request (e.g. I need to do this for every record in Pubmed) and can help
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
how is this query itself originating?
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
I was able to come up with a workaround using the requests library: import requests pmid = 30134295 url = 'https://pubmed.ncbi…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Thanks for you answer! Actually I have already filtered my peak according to blacklist by bedtools. You mean it's meaningless to compare on…
Answer: Redirection of Duplicate PMIDs
by
GenoMax
141k
More than likely not since the database query seems to work for the redirected PMID but not the original. $ esearch -db pubmed -query …
Comment: DYH17 Structure Prediction
by
anasjamshed
▴ 120
Blast showed PDB: 8J07_n9(human) as best template with 62.99%. I also used swissmodel to model the protein and it showed: https://swissmod…
Comment: How to slice a gvcf file with tabix?
by
Pierre Lindenbaum
161k
No, in haplotypecaller
Comment: How to slice a gvcf file with tabix?
by
Sd
• 0
Then what is the best way to do slicing for 1Mb windows? Doing `--intervals` in the GenomicsDBImport?
Comment: How to slice a gvcf file with tabix?
by
Pierre Lindenbaum
161k
> What is your suggestion to run GenomicsDBImport efficiently? call the GVCF by slices eg: chr1:1000000-2000000<br> run GenomicsDBImport …
Comment: How to slice a gvcf file with tabix?
by
Sd
• 0
I want to run gatk `GenomicsDBImport` tool to build a GenomicsDB. I want to slice it to reduce the computation time since I have 1300 gvcf …
Comment: Problem to remove subset of patients with plink
by
chrchang523
10k
The first step has to be taken outside of PLINK here. E.g. append "_1" and "_2" to the duplicated IDs in the .ped or .fam file, then menti…
Comment: Error in cnetplot enrichplot package
by
Ram
43k
Show us the exact call to `cnetplot()` with a sample of all input parameters. Did you compare notes with your friend?
Answer: How to slice a gvcf file with tabix?
by
Pierre Lindenbaum
161k
why would you need to slice a gvcf file ? all the tools in gatk can use a BED / interval / chromosome to narrow the analysis
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