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1,000 results • Page
2 of 20
Sort: Views
Rank
Views
Votes
Replies
4
votes
9
replies
13k
views
Seqtk subseq: structure of file name.lst
sequence
next-gen
updated 6.1 years ago by
Ram
44k • written 6.1 years ago by
ste.lu
▴ 80
1
vote
2
replies
13k
views
kart file in prefetch
rna-seq
updated 7.5 years ago by
Biostar
20 • written 7.7 years ago by
zh.khodadadi
▴ 20
2
votes
13
replies
12k
views
8 follow
(ERR): bowtie2-align exited with value 1
software error
RNA-Seq
updated 6.3 years ago by
basucsmcri
• 0 • written 7.3 years ago by
biostarsb
▴ 30
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
ncbi
nBLAST
linux
blast
updated 20 months ago by
Ram
44k • 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
3
votes
8
replies
12k
views
6 follow
How do I go from UniProt ID to retrieving the gene name?
sequence
6.5 years ago by
a.rex
▴ 350
0
votes
1
reply
12k
views
PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
plink
updated 7.8 years ago by
Biostar
20 • written 7.8 years ago by
rednalf
▴ 90
3
votes
2
replies
12k
views
ExAC PLI score calculation
DNA-Seq
7.2 years ago by
jonessara770
▴ 240
2
votes
13
replies
12k
views
MarkDuplicates memory issue
alignment
Picard
MarkDuplicates
8.4 years ago by
cacampbell
▴ 60
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 6.7 years ago by
Satyajeet Khare
★ 1.6k • written 6.7 years ago by
SMILE
▴ 180
6
votes
7
replies
12k
views
bedtools intersect bed and vcf, coordinates problem
bedtools
bed
vcf
7.1 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
8.0 years ago by
BioICoder
▴ 40
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 11 months ago by
Ram
44k • written 5.2 years ago by
Star
▴ 60
1
vote
2
replies
12k
views
Downloading BAM files GEO/SRA
bam
sra
geo
samtools
sratoolkit
7.8 years ago by
ilobelo
▴ 10
0
votes
4
replies
12k
views
Convert .gbf file to .gbk or .gff
gbk
gff
gbf
updated 16 months ago by
Ram
44k • written 9.0 years ago by
che.bellaj
• 0
4
votes
14
replies
12k
views
All the reads aligned using STAR have low mapping quality (0-3). What is happening?
mapping quality
STAR
BWA
alignment
7.8 years ago by
kirannbishwa01
★ 1.6k
2
votes
3
replies
11k
views
converting maf to vcf
Exome
maf2vcf
updated 16 months ago by
Ram
44k • written 9.0 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
12.7 years ago by
Lisanne
• 0
4
votes
7
replies
11k
views
Grab Coordinate Of Centromeres From Ucsc
ucsc
11.0 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
12.3 years ago by
Nickengland
▴ 130
2
votes
4
replies
11k
views
Pymol-Generate Pymol Movie To Mpeg
pymol
updated 2.3 years ago by
Ram
44k • written 12.3 years ago by
Reyhaneh
▴ 530
5
votes
9
replies
11k
views
Error with samtools faidx...Different line length in sequence
samtools
faidx
updated 6.0 years ago by
Biostar
20 • written 6.2 years ago by
oars
▴ 200
4
votes
11
replies
11k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF
snp
21 months ago by
prasundutta87
▴ 660
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 4 weeks ago by
Ram
44k • written 6.9 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 2.2 years ago by
Ram
44k • written 9.4 years ago by
c.v.oflynn
▴ 100
2
votes
8
replies
11k
views
Plotting different gene ontology categories in a barplot
HI
Gene ontology
R
updated 22 months ago by
zx8754
11k • written 3.3 years ago by
aradhana
• 0
7
votes
8
replies
11k
views
Picard tools duplicate removal
RNA-Seq
picard-tools
6.6 years ago by
blur
▴ 280
3
votes
6
replies
11k
views
6 follow
How to calculate genetic correlation with R
R
updated 2.0 years ago by
ibomsolomon
• 0 • written 10.0 years ago by
Tohamy
▴ 80
2
votes
2
replies
11k
views
How to make clusters in heat map using ggplot2?
RNA-Seq
rna-seq
R
5.1 years ago by
John
▴ 270
5
votes
2
replies
11k
views
Turning Seq objects into strings
sequence
5.2 years ago by
schlogl
▴ 160
3
votes
2
replies
10k
views
BWA-MEM Vs BWA-ALN
next-gen
genome
alignment
8.0 years ago by
SOHAIL
▴ 400
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 2.4 years ago by
Ram
44k • written 9.8 years ago by
trakhtenberg
▴ 160
0
votes
0
replies
10k
views
pheatmap row annotation and title font size questions
heatmap
pheatmap
updated 16 months ago by
Ram
44k • written 9.0 years ago by
neokao
• 0
3
votes
1
reply
10k
views
Negative P-Values
gene
genome
next-gen-sequencing
updated 21 months ago by
Ram
44k • written 8.7 years ago by
stevenlang123
▴ 210
2
votes
4
replies
10k
views
num_threads with blastn in blast 2.6.0+
blast
5.4 years ago by
navela78
▴ 70
2
votes
8
replies
10k
views
Size of typical genomic data
genomic
updated 14 months ago by
Ram
44k • written 6.0 years ago by
Nicolas Rosewick
11k
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
6.2 years ago by
DanielC
▴ 170
7
votes
9
replies
10k
views
Samtools Index Segmentation Fault
samtools
index
10.2 years ago by
Noushin N
▴ 600
2
votes
1
reply
10k
views
Calculate Linkage Disequilibrium For Snps (Using R^2)
snp
linkage
10.9 years ago by
TitoPullo
▴ 180
1
vote
2
replies
10k
views
Converting MSTRG from stringtie with gene name
RNA-Seq
Stringtie
updated 6.4 years ago by
Biostar
20 • written 6.4 years ago by
fhassanz
▴ 20
3
votes
3
replies
10k
views
bcftools mpileup output format
bcftools
mpileup
5.7 years ago by
tarek.mohamed
▴ 360
3
votes
4
replies
10k
views
Aligning RNA seq data to genome or transcriptome
RNA-Seq
ngs
transcriptome
genome
updated 6.7 years ago by
Ram
44k • written 6.7 years ago by
KVC_bioinfo
▴ 590
1
vote
5
replies
10k
views
What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With Gatk?
bed
agilent
gatk
updated 4.3 years ago by
Karma
▴ 310 • written 10.5 years ago by
newDNASeqer
▴ 760
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 3.4 years ago by
dqq102829
• 0 • written 4.4 years ago by
zhangdengwei
▴ 210
0
votes
0
replies
10k
views
Map Between Uniprot Accesion And Gene.Symbol Using R Or/And Mysql
r
bioconductor
mysql
10.4 years ago by
jfertaj
▴ 110
6
votes
8
replies
10k
views
7 follow
Converting SNP names from Illumina GSA array to rsID using PLINK
SNP
plink
6.6 years ago by
dam4l
▴ 200
3
votes
5
replies
10k
views
pheatmap: how to avoid fontface, fontsize, and color from writing over existing rownames
fontsize
rows
color
R
pheatmap
updated 3.0 years ago by
cpad0112
21k • written 3.0 years ago by
ladypurrsia
▴ 60
1
vote
1
reply
10k
views
Raxml bootstrap support values
figtree
raxml
bootstrap
updated 2.6 years ago by
Ram
44k • written 10.0 years ago by
JackBel
• 0
1,000 results • Page
2 of 20
Recent Votes
Comment: Problem in getting geo file through GEOQUERY
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
Answer: Functional enrichment analysis for unique gene IDs
Comment: Super ehancers
Comment: Why does assigning genes with biomart give me different values than using a tran
Comment: Multiplexing for pooled CRISPR screen sequencing
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
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Recent Replies
Answer: Add stats to the plot
by
Ghada
• 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",comparis…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
LChart
3.9k
I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Basically this is my code: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # # pkgs <- rowna…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
If that were the case, I would expect there not to be any uncalled sites in the vcf, yet there are a large number of sites with "." placeho…
Comment: Problem in getting geo file through GEOQUERY
by
bk11
★ 2.5k
It just runs fine for me with just a single line of code. library(GEOquery) GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE) …
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
Dave Carlson
★ 1.7k
I can't speak to UnifiedGenotyper, as it has been many years since GATK stopped supporting it, and I have not used it in a long time. But …
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
I want to get lot of files through code
Comment: Problem in getting geo file through GEOQUERY
by
GenoMax
142k
Query seems to be timing out. Try getting the file directly here: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1145/matrix/GSE1145-GP…
Comment: Add stats to the plot
by
Ghada
• 0
Thanks for the help. Unfortunately, did not work :( error in asserttat_group_columns_exists(data) : data should contain group1 and grou…
Comment: downloading chemical database from ChEMBL
by
GenoMax
142k
How about following https://www.ebi.ac.uk/chembl/web_components/explore/activities/ --> Select a compound --> Related Targets button --> D…
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
As a follow-up, is it possible to get a variant call with UnifiedGenotyper if rather than N, I have one of the ambiguity codes (e.g. R, Y, …
Answer: Allele count of 2 for homoplasmic MT variants in VCF
by
LChart
3.9k
The GATK (and afaik every caller that I know) treats every contig of the reference as having the same ploidy (so all haploid, all diploid, …
Comment: Where are the illumina adapters on Trimmomatic take from?
by
GenoMax
142k
Use the sequence Illumina recommends for the specific kit.
Comment: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
> Thanks. What determines what constitutes a good distance? I think tools like BWA use the median distance for each chunk of processed d…
Comment: Where are the illumina adapters on Trimmomatic take from?
by
bioinfo
▴ 150
Thank you for the explanation. Is it more appropriate then to use the sequence from the illumina documentation or the one from the github?
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