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274 results • Page
1 of 6
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6
votes
5
replies
9.6k
views
Forum:
Single-end sequencing versus paired-end
Assembly
snp
sequencing
updated 5 hours ago by
Ram
39k • written 3.3 years ago by
Sujata
▴ 20
9
votes
1
reply
7.0k
views
Forum:
Master in statistics or bioinformatics
masters
career
statistics
updated 1 hour ago by
Ram
39k • written 9.1 years ago by
indeci
▴ 50
12
votes
23
replies
6.6k
views
6 follow
motif search with ATAC-seq
motif-search
ATAC-seq
updated 5 hours ago by
Ram
39k • written 4.7 years ago by
grant.hovhannisyan
★ 2.5k
6
votes
5
replies
6.3k
views
Forum:
Converting GFF to GTF
GTF
GFF
updated 2 hours ago by
Ram
39k • written 3.2 years ago by
Juke34
7.9k
4
votes
3
replies
5.4k
views
ATACseq alignment issues
BWA
alignment
ATAC-seq
updated 5 hours ago by
Ram
39k • written 7.5 years ago by
kaivalya.shevade
• 0
1
vote
8
replies
5.0k
views
Forum:
Would you use sci-hub's mirror site?
sci-hub
updated 7 hours ago by
Ram
39k • written 3.4 years ago by
cduukj
• 0
3
votes
4
replies
4.7k
views
How to get the gene expression matrix from GEO while getGEO returns 0 features?
GETquery
ATAC-seq
GEO
getGEO
RNA-Seq
updated 5 hours ago by
Ram
39k • written 3.9 years ago by
bioyas
▴ 10
4
votes
5
replies
3.9k
views
macs2 normalization on broadPeak
callpeak
atac-seq
macs2
updated 5 hours ago by
Ram
39k • written 5.9 years ago by
firatuyulur
▴ 320
10
votes
14
replies
3.8k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 5 hours ago by
Ram
39k • written 3.3 years ago by
gable_works
▴ 50
6
votes
8
replies
3.6k
views
7 follow
Which method is the best for using in "dba.count" in Diffbind R package
ChIP-Seq
diffbind
updated 9 hours ago by
Rory Stark
★ 1.8k • written 3.7 years ago by
m.sadman.sakib
▴ 120
5
votes
5
replies
3.5k
views
How to create SAF from text file for FeatureCounts
featureCounts
ATAC-seq
updated 5 hours ago by
Ram
39k • written 2.1 years ago by
pt.taklifi
▴ 60
4
votes
6
replies
3.1k
views
convert gbk to fasta
genome
updated 6 hours ago by
Ram
39k • written 3.4 years ago by
wellinsantos84
▴ 10
3
votes
3
replies
2.9k
views
Normalize BigWig's for # of reads in peaks and sequencing depth
Deeptools
ATAC-seq
updated 5 hours ago by
Ram
39k • written 3.3 years ago by
Zeel
• 0
0
votes
2
replies
2.8k
views
How to run Picard docker image
next-gen
alignment
docker
picard
updated 22 hours ago by
geocarvalho
▴ 330 • written 3.7 years ago by
elcortegano
▴ 180
1
vote
7
replies
2.7k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT
TF-footprinting
ATAC-seq
updated 5 hours ago by
Ram
39k • written 4.5 years ago by
grant.hovhannisyan
★ 2.5k
2
votes
1
reply
2.4k
views
News:
RNAseq data analysis with R/ Bioconductor - ONLINE COURSE
R
RNA-Seq
Bioconductor
updated 1 hour ago by
Ram
39k • written 3.2 years ago by
carlopecoraro2
★ 2.3k
8
votes
8
replies
2.3k
views
News:
Coronavirus Genome Analysis: a new volume in the Biostar Handbook
biostar-handbook
education
updated 3 hours ago by
Ram
39k • written 3.3 years ago by
Istvan Albert
98k
4
votes
9
replies
2.3k
views
How to view bigwig files in UCSC with windowed coverage?
ucsc
atac-seq
ChIP-Seq
updated 5 hours ago by
Ram
39k • written 3.5 years ago by
fr
▴ 200
6
votes
4
replies
2.1k
views
Forum:
Ru/Read Until in Nanopore sequencers
Oxford-Nanopore
alignment
sequencing
updated 4 hours ago by
Ram
39k • written 3.3 years ago by
jean.elbers
★ 1.7k
0
votes
3
replies
2.1k
views
Picard's Tool MarkDuplicates problem
picard
updated 4 hours ago by
Ram
39k • written 3.3 years ago by
harmadikemil
• 0
16
votes
10
replies
2.0k
views
Forum:
Asking for feedback on a Python library for computing alignments
alignment
Python
updated 10 hours ago by
Alexander
▴ 70 • written 16 months ago by
bernhard.liebl
▴ 60
7
votes
8
replies
2.0k
views
Forum:
Virus Genome Length and GC Content of SARS-COV-2 causing COVID-19
sequence
genome
updated 1 hour ago by
Ram
39k • written 3.2 years ago by
dulankak
▴ 30
29
votes
18
replies
2.0k
views
12 follow
Forum:
what are the big questions in bioinformatics field nowadays
genome
updated 4 hours ago by
Ram
39k • written 3.3 years ago by
t4192
▴ 20
2
votes
2
replies
2.0k
views
get count matrix from bam files
bam
ATAC-seq
updated 5 hours ago by
Ram
39k • written 2.1 years ago by
pt.taklifi
▴ 60
1
vote
7
replies
1.9k
views
Job:
PhD scholarship in Bioinformatics, Rostock University Medical Center (Rostock, Germany)
PhD
scholarship
updated 4 hours ago by
Ram
39k • written 3.3 years ago by
Israel Barrantes
▴ 790
0
votes
6
replies
1.9k
views
Variable read length distribution after cutadapt running for my ATAC-seq datasets
cutadapt
read-length
alignment
ATAC-seq
updated 5 hours ago by
Ram
39k • written 3.1 years ago by
yaoyao20152031
• 0
4
votes
2
replies
1.9k
views
Forum:
wet-lab vs dry-lab scientists
cv
language
updated 4 hours ago by
Ram
39k • written 3.3 years ago by
igor
13k
0
votes
3
replies
1.9k
views
METAL (gwas meta-analysis tool)
meta-analysis
gwas
metal
genomics
updated 6 hours ago by
Ram
39k • written 3.4 years ago by
bigfoot
▴ 10
2
votes
0
replies
1.8k
views
Job:
Research Scientist in Bioinformatics - Brigham and Women's Hospital, Harvard Medical School
Genomics
Neuroscience
Boston
updated 1 hour ago by
Ram
39k • written 3.2 years ago by
Xianjun
▴ 310
0
votes
4
replies
1.8k
views
Spatial transcriptomics without the h5 file
h5
spatial-transcriptomics
updated 3 hours ago by
Arvin
• 0 • written 17 months ago by
jordi.diaz-manera
▴ 10
1
vote
2
replies
1.7k
views
Job:
Bioinformatics Analyst/Bioinformatics Research Scientist (Van Andel Institute)
research-scientist
analyst
updated 3 hours ago by
Ram
39k • written 3.2 years ago by
deanpett
▴ 20
0
votes
2
replies
1.7k
views
How to handle NaN in emmax Kinship matrix?
GWAS
SNP
updated 12 hours ago by
Thu
• 0 • written 5.1 years ago by
CWesse
• 0
1
vote
5
replies
1.6k
views
Wrong coordinates of peaks in DiffBind
DiffBind
ATAC-seq
updated 5 hours ago by
Ram
39k • written 4.7 years ago by
grant.hovhannisyan
★ 2.5k
31
votes
41
replies
1.6k
views
12 follow
Forum:
Question regarding journal publications
publications
journals
updated 4 hours ago by
Ram
39k • written 3.3 years ago by
K.Gee
▴ 40
0
votes
0
replies
1.6k
views
Job:
Computational Biology Principal Scientist @ Boehringer-Ingelheim Vienna
data-science
computational-biology
updated 4 hours ago by
Ram
39k • written 2.7 years ago by
christian.haslinger
• 0
4
votes
4
replies
1.6k
views
how to identify disease variants from bam file ?
disease-variants
VCF
bam
ATAC-seq
updated 5 hours ago by
Ram
39k • written 4.5 years ago by
masaver
▴ 20
6
votes
5
replies
1.5k
views
Forum:
Stanford HCP MS Biomedical Informatics vs Johns Hopkins MS Bioinformatics
career
updated 4 hours ago by
Ram
39k • written 3.3 years ago by
melissachua90
▴ 40
6
votes
13
replies
1.5k
views
News:
Ensembl reduced functionality: 10th March-16th April 2020
BLAT
VEP
Ensembl
service
updated 4 hours ago by
Ram
39k • written 3.3 years ago by
Ben_Ensembl
★ 2.2k
1
vote
2
replies
1.5k
views
News:
NCBI Datasets - try it out!
Assembly
refseq
genome
ncbi
updated 1 hour ago by
Ram
39k • written 3.2 years ago by
vkkodali_ncbi
★ 3.5k
2
votes
4
replies
1.4k
views
What is the best way to analyze and enrich a list of DE genes from RNAseq?
R
pathways
enrichment
RNA-Seq
updated 1 hour ago by
Ram
39k • written 3.2 years ago by
mario.red8976
▴ 110
0
votes
0
replies
1.4k
views
Job:
Postdoc / PhD student comparative genomics / population genomics of plant pathogens, Munich Germany
assembly
R
Nanopore
next-gen
updated 7 hours ago by
Ram
39k • written 3.4 years ago by
stam
• 0
4
votes
0
replies
1.4k
views
Job:
PhD studentship in bioinformatics: Network Inference and Systems Biology
network-biology
updated 7 hours ago by
Ram
39k • written 3.4 years ago by
erik.sonnhammer
▴ 40
1
vote
1
reply
1.4k
views
How to analyze DNA data with UMI
next-gen-sequencing
umi
updated 1 hour ago by
Ram
39k • written 3.2 years ago by
deniselavezzari
• 0
0
votes
0
replies
1.4k
views
Job:
Postdoc position in computational biology, Dessimoz Lab, University of Lausanne & SIB
postdoc
switzerland
updated 1 hour ago by
Ram
39k • written 3.2 years ago by
Christophe Dessimoz
▴ 740
2
votes
0
replies
1.4k
views
Job:
Bioinformatician // Foodome, Inc. // (Remote, Full-Time)
foodome
remote
updated 1 hour ago by
Ram
39k • written 2.9 years ago by
Foodome Team
▴ 20
2
votes
0
replies
1.4k
views
Job:
Postdoctoral Scientist Position in Computational Biology at University of Missouri
scRNAseq
postdoc
ChIP-Seq
updated 5 hours ago by
Ram
39k • written 3.3 years ago by
Obi Griffith
20k
0
votes
1
reply
1.3k
views
Job:
Bioinformatics Scientist/Programmer, Clinical Cancer Genomics Laboratory at UCSF
next-gen-sequencing
R
snp
RNA-Seq
updated 7 hours ago by
Ram
39k • written 3.4 years ago by
ccglucsf
▴ 20
2
votes
1
reply
1.3k
views
Job:
Bioinformatics Scientist (North Bethesda, MD)
genetics
computational-biology
updated 6 hours ago by
Ram
39k • written 3.4 years ago by
dlbrodginski
• 0
3
votes
4
replies
1.3k
views
Job:
GSK Data Strategy & Design Expert
NGS
DATA
R
GSK
updated 6 hours ago by
Ram
39k • written 3.3 years ago by
pichai.raman
▴ 40
0
votes
0
replies
1.3k
views
Job:
Offering a bioinformatics post Doc/PhD position for clinical cancer epigenomics (Berlin, Germany)
dna-methylation
machine-learning
updated 4 hours ago by
Ram
39k • written 2.7 years ago by
naveed.ishaque
• 0
274 results • Page
1 of 6
Recent Votes
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
A: Mouse promoter regions
Answer: How to get information about promoter from bulk-RNAseq?
A: Extracting Flanking Regions across TSS using R scripts
A: Mouse promoter regions
A: Finding zebrafish promoters ENSEMBL
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Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq?
by
rpolicastro
12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq?
by
Trivas
★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap?
by
Ram
39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag
by
Ram
39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R
by
rohitsatyam102
▴ 690
Hi Were u able to achieve this?
Comment: Differences in GTF files hg19 and hg38
by
GenoMax
130k
Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have be…
Comment: VCF file CSQ flag
by
Pierre Lindenbaum
154k
if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.f…
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Ram
39k
https://www.biostars.org/u/127538/ : Please delete this question or it will be deleted by moderators in a few days.
Comment: VCF file CSQ flag
by
Ram
39k
A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci wit…
Comment: Differences in GTF files hg19 and hg38
by
heureuse
• 0
Thank you very much. I get it from UCSC.
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Arup Ghosh
3.2k
This post does not fit the theme of this forum.
Comment: CellRanger problem
by
Arup Ghosh
3.2k
Try with atleast 32 GB of Memory rather than 16 GB specified by `limitGenomeGenerateRAM` option.
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