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116,620 results • Page
1 of 2333
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Votes
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0
votes
5
replies
186
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Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated just now by
Pierre Lindenbaum
161k • written 9 hours ago by
J
• 0
19
votes
10
replies
14k
views
9 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 3 hours ago by
benformatics
3.9k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
2
replies
135
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 2 hours ago by
dsull
★ 5.8k • written 9 hours ago by
Aaliya
▴ 10
2
votes
0
replies
54
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
scRNA
Machinelearning
GenerativeAI
4 hours ago by
Claire Watson
▴ 50
0
votes
2
replies
134
views
Rare Disease Variant Pathway Analysis
Pathway
analysis
4 hours ago by
The_PyPanda
▴ 10
0
votes
0
replies
60
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
5 hours ago by
HarperReed
• 0
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
2
replies
80
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 2 hours ago by
GenoMax
141k • written 5 hours ago by
sapuizait
▴ 10
1
vote
0
replies
45
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
7 hours ago by
KABILAN
▴ 50
0
votes
0
replies
45
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
7 hours ago by
SineWave
• 0
0
votes
0
replies
44
views
RNA-seq: full length gene
identification
gene
full
length
8 hours ago by
Nargis
• 0
0
votes
1
reply
73
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 9 hours ago by
Jeremy Leipzig
22k • written 10 hours ago by
zihanss
• 0
0
votes
0
replies
41
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
10 hours ago by
turcoa1
• 0
3
votes
3
replies
172
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 16 hours ago by
swbarnes2
14k • written 22 hours ago by
M
• 0
0
votes
0
replies
61
views
Designing single-stable RNA molecules
structure
RNA
17 hours ago by
Edna
• 0
0
votes
0
replies
69
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
17 hours ago by
simplitia
▴ 130
0
votes
1
reply
107
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 18 hours ago by
ATpoint
82k • written 18 hours ago by
AaronJaime
• 0
0
votes
2
replies
167
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 19 hours ago by
GenoMax
141k • written 1 day ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
192
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 16 hours ago by
Ram
43k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
130
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 17 hours ago by
Ram
43k • written 1 day ago by
Francesco
▴ 10
1
vote
4
replies
180
views
ScRNA data question
scRNA
Vlnplot
Samples
1 hour ago by
starswillfade
▴ 10
0
votes
0
replies
74
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
21 hours ago by
avocado123
• 0
0
votes
0
replies
69
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 17 hours ago by
Ram
43k • written 21 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
64
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
21 hours ago by
Emily
▴ 10
1
vote
0
replies
81
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
21 hours ago by
rohitsatyam102
▴ 850
0
votes
0
replies
66
views
how to read graph_test output of monocle 3
monocle3
22 hours ago by
synat.keam
▴ 100
0
votes
0
replies
89
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
22 hours ago by
Assaf
• 0
0
votes
1
reply
398
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 23 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
3
votes
4
replies
229
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
18 hours ago by
QX
• 0
2
votes
1
reply
155
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 1 day ago by
Adrian Altenhoff
★ 1.1k • written 1 day ago by
hemantcnaik
• 0
0
votes
0
replies
83
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
1 day ago by
Aspire
▴ 300
2
votes
4
replies
231
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 17 hours ago by
Ram
43k • written 1 day ago by
ashaneev07
▴ 20
2
votes
3
replies
195
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
analyst
▴ 30
0
votes
1
reply
134
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 1 day ago by
b.contreras.moreira
▴ 170 • written 1 day ago by
Broccoli
• 0
0
votes
2
replies
163
views
Highest variable features in single cell data
single-cell
updated 17 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
1
reply
162
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 1 day ago by
Scooter
▴ 280 • written 2 days ago by
Akash D
▴ 40
2
votes
4
replies
2.3k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 1 day ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
0
votes
2
replies
194
views
PCA plot
DESeq2
PCAplot
updated 5 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
1
reply
163
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 17 hours ago by
Ram
43k • written 1 day ago by
Ming Tommy Tang
★ 3.9k
0
votes
3
replies
301
views
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 17 hours ago by
Ram
43k • written 3 days ago by
qudrat.nii
▴ 10
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 1 day ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
0
replies
106
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
1 day ago by
4fzcgueyp5
• 0
2
votes
3
replies
285
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 3 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
emmanouil.a
▴ 120
0
votes
2
replies
213
views
Annovar using R package
Annovar
gnomAD
R
17 hours ago by
DKA
▴ 40
0
votes
2
replies
195
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
biochugs
• 0
3
votes
8
replies
510
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
Aaliya
▴ 10
1
vote
8
replies
766
views
Adding CB tag to bam file
samtools
bam
updated 1 day ago by
Pierre Lindenbaum
161k • written 7 days ago by
Maria
• 0
1
vote
10
replies
907
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
1 day ago by
DKA
▴ 40
0
votes
2
replies
797
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 1 day ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
5
replies
290
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
116,620 results • Page
1 of 2333
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Comment: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Is there a software that can compare phylogenetic trees to each othe (face to fa
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
Converting between Ensembl Versions
Comment: what is the purpose of indexing the reference genome (Kallisto)
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Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
by
starswillfade
▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
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 …
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