Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
1,000 results • Page
2 of 20
Sort: Views
Rank
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 6.3 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 7.8 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
6.5 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
7.1 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
43k • written 5.1 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
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
7.8 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 2.3 years ago by
Ram
43k • 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 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 9 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
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
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
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
11k
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
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
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
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 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
6.1 years ago by
DanielC
▴ 170
2
votes
4
replies
10k
views
num_threads with blastn in blast 2.6.0+
blast
5.4 years ago by
navela78
▴ 70
7
votes
9
replies
10k
views
Samtools Index Segmentation Fault
samtools
index
10.1 years ago by
Noushin N
▴ 600
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
2 of 20
Recent Votes
Comment: what is the purpose of indexing the reference genome (Kallisto)
Answer: what is the purpose of indexing the reference genome (Kallisto)
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Recent Locations •
All
Netherlands,
just now
Hong Kong,
1 minute ago
United States,
3 minutes ago
UCLA,
4 minutes ago
Spain,
5 minutes ago
United States,
6 minutes ago
USA,
6 minutes ago
Recent Awards •
All
Popular Question
to
sil_bioinfo
▴ 40
Popular Question
to
sapuizait
▴ 10
Voter
to
analyst
▴ 30
Scholar
to
ATpoint
82k
Popular Question
to
zdiazmar
▴ 30
Popular Question
to
hkarakurt
▴ 180
Student
to
John Torcivia
▴ 70
Recent Replies
Comment: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
i.sudbery
19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto)
by
dsull
★ 5.8k
I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
Jalil Sharif
▴ 80
The updated code in R using rtracklayer for reading a gtf file. https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
Comment: Rare Disease Variant Pathway Analysis
by
The_PyPanda
▴ 10
Thank you LauferVA, Your advice has been useful and I now a lot to think about and read. Also, I just wanted to clarify I do not ha…
Comment: CDS vs cDNA vs transcript for mapping RNA-Seq reads
by
Antonio R. Franco
★ 5.1k
You cannot do it with Kallisto either. In fact, the indexation will fail in attempting to index a genome file
Comment: PCA plot
by
ATpoint
82k
What is your question? Add details and clarity. Ask a precise question and please avoid opening more questions on the same underlying issue…
Comment: genome assembly records not present in assembly_summary.txt
by
Joe
21k
If you have the accession numbers can you not use something like `eutils`?
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
> Next, I tried using bedtools window but in your original post you said > tried finding the intersection of these bed files using bedto…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
Thank you very much! I tried it out! This is a handy tool useful for many different applications, and in regards to my problem - although …
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
> using bcftools Show us what you tried
Answer: gvcf joint calling
by
Jeremy Leipzig
22k
> Hi, guys, there is a question about the genomic gVCF file. I wonder > that since gVCF contains the non-var block records, why after merge…
Comment: Missing protein (VEGF-A) in String db
by
shalespringer
• 0
Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
Traffic: 2557 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6