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1,000 results • Page
4 of 20
Sort: replies
Rank
Views
Votes
Replies
12
votes
22
replies
2.5k
views
Help with error in GATK variant calling
GATK
updated 11 months ago by
Ram
43k • written 11 months ago by
Chris
▴ 260
9
votes
22
replies
9.7k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
9 months ago by
vytarasov
▴ 180
11
votes
22
replies
4.6k
views
7 follow
Which New Bioinformatics Related Tool Would You Appreciate The Most?
programming
updated 9 months ago by
Ram
43k • written 11.8 years ago by
Biomonika (Noolean)
3.2k
138
votes
22
replies
65k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene
LIMMA
edgeR
updated 10 months ago by
Kevin Blighe
87k • written 6.4 years ago by
Mike
★ 1.9k
57
votes
22
replies
28k
views
7 follow
Batch correction in DESeq2
Combat
DESeq2
Batch-Effect
updated 17 days ago by
Ram
43k • written 4.5 years ago by
Arindam Ghosh
▴ 510
81
votes
21
replies
42k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed
transcript
ucsc
biomart
updated 7 months ago by
Joel Wallenius
▴ 210 • written 10.2 years ago by
pristanna
▴ 750
43
votes
21
replies
5.4k
views
9 follow
Helping Biostar Grow
biostars
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 10 months ago by
Ram
43k • written 8.0 years ago by
John
13k
39
votes
21
replies
13k
views
10 follow
Forum:
Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.5 years ago by
Juke34
8.5k
27
votes
21
replies
38k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 6 months ago by
Axzd
▴ 70 • written 9.8 years ago by
onter
▴ 170
18
votes
21
replies
4.4k
views
Tool:
uQ - small binary FASTQ
Compression
FASTQ
updated 10 months ago by
Ram
43k • written 7.1 years ago by
John
13k
80
votes
21
replies
36k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 5 months ago by
kathryn.jacksonjones
• 0 • written 10.0 years ago by
M K
▴ 660
16
votes
21
replies
9.9k
views
7 follow
How to extract bigWig signal for a given bed file?
bigWig
updated 8 months ago by
Ram
43k • written 7.5 years ago by
Bioradical
▴ 60
13
votes
21
replies
1.8k
views
Practical Haplotype Graph Paths
practical-haplotype-graph
PHG
updated 10 weeks ago by
pjb39
▴ 200 • written 5 months ago by
micah_k
▴ 10
4
votes
21
replies
2.3k
views
6 follow
how to automate this process
python
plantCARE
updated 10 months ago by
Ram
43k • written 7.2 years ago by
ashish
▴ 680
4
votes
21
replies
2.6k
views
Limma returned only positive logFC values
edgeR
differential-expression
deg
limma
10 months ago by
melissachua90
▴ 60
23
votes
21
replies
8.8k
views
9 follow
fastest UMAP method
UMAP
R
updated 5 months ago by
Mensur Dlakic
★ 27k • written 4.5 years ago by
grey
▴ 30
22
votes
21
replies
4.8k
views
7 follow
Quick Programming Challenge: Calculate Common And Unique Regions From A List Of Chromosome Segments
programming
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Khader Shameer
18k
10
votes
21
replies
3.2k
views
How to interpret heatmap using plotheatmap from deeptools?
ATAC-seq
deeptools
8 months ago by
Chris
▴ 260
48
votes
21
replies
5.1k
views
9 follow
What Online Gene-Centric Resources Do You Use?
gene
database
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Andrew Su
4.9k
12
votes
21
replies
6.6k
views
7 follow
Illumina HumanHT-12 V4.0 expression beadchip
R
lumi
LIMMA
updated 5 months ago by
Gordon Smyth
★ 7.0k • written 4.1 years ago by
zelda
▴ 50
14
votes
21
replies
10k
views
7 follow
HOMER annotatePeaks.pl problem
RNA-Seq
ChIP-Seq
HOMER
updated 10 months ago by
Ram
43k • written 6.6 years ago by
Seq225
▴ 110
13
votes
21
replies
3.0k
views
6 follow
Aberrant splicing in bulk RNAseq
aberrant-splicing
transcript
isoform
exon
updated 11 months ago by
sbt_gvs
• 0 • written 14 months ago by
txema.heredia
▴ 110
60
votes
21
replies
3.8k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome
assembly
updated 7 months ago by
Michael
54k • written 7 months ago by
sqshigg
▴ 60
52
votes
21
replies
49k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 10 months ago by
Ram
43k • written 12.1 years ago by
Geparada
★ 1.5k
15
votes
21
replies
5.5k
views
7 follow
alphafold online availability and use case
alphafold
structure
prediction
written 2.7 years ago by
gnmcsbnfrmtcsclb
▴ 70
5
votes
21
replies
2.9k
views
How to get my tool on Homebrew ?
homebrew
pipeline
updated 10 months ago by
Ram
43k • written 4.8 years ago by
Elephantdumbo
▴ 20
24
votes
21
replies
7.5k
views
9 follow
News:
Misunderstood parameter of NCBI BLAST
blast
alignment
updated 11 months ago by
Ram
43k • written 5.6 years ago by
Farbod
★ 3.4k
0
votes
21
replies
1.0k
views
Expression analysis of LncRNA from RNA-seq data
expression
lncrna
10 weeks ago by
analyst
▴ 20
21
votes
20
replies
9.1k
views
11 follow
Laptops for bioinformatics
hardware
Laptops
updated 10 months ago by
LauferVA
4.2k • written 17 months ago by
tsomakiank
▴ 40
16
votes
20
replies
14k
views
7 follow
Extracting allele, Genotype from VCF file
vcf
updated 10 months ago by
Ram
43k • written 6.0 years ago by
sukhjindermultani85
▴ 20
83
votes
20
replies
19k
views
17 follow
How Do Pathway Databases Compare?
pathway
database
subjective
updated 9 months ago by
Peter Karp
▴ 30 • written 13.5 years ago by
Shigeta
▴ 470
7
votes
20
replies
2.1k
views
Forum:
NGS RNA-Seq Analysis Pipeline Tophat vs STAR
STAR
RNA-Seq
TopHat
updated 11 months ago by
Ram
43k • written 3.3 years ago by
mikefeixu
▴ 10
29
votes
20
replies
3.6k
views
Tool:
FastQt : a clone of FastQC in C++/Qt
fastqc
Cpp
fastq
Qt
updated 10 months ago by
Ram
43k • written 7.4 years ago by
sacha
★ 2.4k
28
votes
20
replies
21k
views
7 follow
how do I run repeat masker
repeatmasker
updated 3 months ago by
Andrzej Zielezinski
11k • written 8.4 years ago by
ksi216
▴ 80
14
votes
20
replies
6.6k
views
7 follow
Tool Recommendations For Human Genome Assembly
assembly
human-genome
updated 10 months ago by
Ram
43k • written 11.2 years ago by
Chris Cole
▴ 800
0
votes
20
replies
1.6k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper
RNA-seq
6 months ago by
langziv
▴ 50
1
vote
20
replies
1.6k
views
randomreads.sh only produces reads for chr1 to chr7
randomreads.sh
bbmap
updated 9 months ago by
GenoMax
141k • written 9 months ago by
berndmann
▴ 10
17
votes
20
replies
1.4k
views
What is the best way to compute genetic distances between FASTQ files?
genetic-distance
fastq
updated 5 months ago by
GenoMax
141k • written 6 months ago by
mikazon
▴ 10
22
votes
20
replies
4.8k
views
Tool:
elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam
bam
bqsr
updated 10 months ago by
Ram
43k • written 5.5 years ago by
Charlotte.Herzeel
▴ 150
15
votes
20
replies
1.7k
views
Bbtools callvariant multisample mode, + base recalibration
Bbtools
5 months ago by
Axzd
▴ 70
18
votes
20
replies
4.1k
views
9 follow
Is There Any Useful Information To Be Gathered Analyzing The Genomes Of Different Populations Of Cicadas?
project
education
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Scott
▴ 70
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 11 days ago by
e.r.zakiev
▴ 200 • written 4.3 years ago by
kevin.stachelek
▴ 80
5
votes
20
replies
4.1k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 13 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
37
votes
20
replies
7.2k
views
14 follow
Online Bioinformatics Resources
online-resources
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
2
votes
20
replies
2.3k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
7 months ago by
Maxine
▴ 40
12
votes
20
replies
2.4k
views
SEACR and MACS2
MACS2
SEACR
updated 9 months ago by
rfran010
▴ 900 • written 9 months ago by
qudrat.nii
▴ 10
18
votes
20
replies
4.4k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray
differential-gene-expression
updated 13 days ago by
Ram
43k • written 7.5 years ago by
morteza.mahmoudisaber
▴ 80
12
votes
20
replies
1.2k
views
Help with gatk BaseRecalibrator
GATK
variant-calling
updated 4 months ago by
Ram
43k • written 4 months ago by
Chris
▴ 260
12
votes
20
replies
2.2k
views
Is there a single header file somewhere I can use to read bam?
cpp
bam
c
updated 11 months ago by
Ram
43k • written 5.5 years ago by
Click downvote
▴ 720
1,000 results • Page
4 of 20
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: 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?
Comment: 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
Comment: Error in cnetplot enrichplot package
by
Farhad
• 0
I check dataframe it has more than 2 columns
Comment: Error in cnetplot enrichplot package
by
Farhad
• 0
We write it to csv and then send it via email
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