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194 results • Page
1 of 4
Sort: Views
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Views
Votes
Replies
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
1 day ago by
Kevin Blighe
87k
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 30 minutes ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 5 days ago by
Ram
43k • written 10.6 years ago by
Louis
▴ 150
10
votes
6
replies
9.8k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 5 hours ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 1 day ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 6 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 22 hours ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
8
votes
5
replies
5.1k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 2 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
2
votes
6
replies
3.6k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 19 hours ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
0
votes
13
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 2 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 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
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 3 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
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
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 1 day ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
8
replies
1.2k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 6 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
5
votes
13
replies
1.1k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 6 days ago by
ATpoint
82k • written 7 days ago by
BioinfGuru
★ 1.7k
2
votes
3
replies
946
views
Method to detect genome doubling
CNV
genome doubling
updated 4 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
1
vote
10
replies
909
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
1 day ago by
DKA
▴ 40
2
votes
9
replies
820
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 2 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
2
replies
798
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 1 day ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
1
vote
8
replies
767
views
Adding CB tag to bam file
samtools
bam
updated 1 day ago by
Pierre Lindenbaum
161k • written 7 days ago by
Maria
• 0
8
votes
15
replies
741
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 12 hours ago by
GenoMax
141k • written 7 weeks ago by
Sofia
• 0
3
votes
3
replies
716
views
KissDE and batch effect
kissDE
kissplice
4 days ago by
david.b.rombaut
▴ 10
2
votes
5
replies
685
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 5 days ago by
Jesse
▴ 740 • written 6 days ago by
Ann
★ 2.4k
3
votes
4
replies
654
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
3 days ago by
rahu
• 0
3
votes
6
replies
644
views
Ciriquant not configuring hisat2 indexed files
ciriquant
4 days ago by
Atul K.
• 0
5
votes
4
replies
622
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
2 days ago by
kirillkirilenko
▴ 40
1
vote
5
replies
589
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 2 days ago by
atowns21
• 0 • written 3 months ago by
benjamin.pyenson
• 0
0
votes
2
replies
581
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 1 day ago by
Dateline
• 0 • written 21 months ago by
JZX
• 0
1
vote
5
replies
560
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 6 days ago by
GenoMax
141k • written 6 days ago by
Luka
• 0
3
votes
5
replies
544
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
4 days ago by
n_navy
• 0
1
vote
0
replies
539
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
6 days ago by
mathavanbioinfo
▴ 90
0
votes
4
replies
523
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 5 days ago by
ATpoint
82k • written 6 days ago by
rheab1230
▴ 140
8
votes
8
replies
521
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
Aaliya
▴ 10
2
votes
5
replies
519
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 5 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
Giorgio
• 0
4
votes
11
replies
512
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 2 days ago by
LauferVA
4.2k • written 3 days ago by
dominickd
• 0
0
votes
3
replies
483
views
python file for coding potential calculator
cpc2.py
updated 3 days ago by
atharvakarkare14
▴ 10 • written 7 days ago by
Ashok
• 0
0
votes
11
replies
470
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
15 hours ago by
atowns21
• 0
3
votes
3
replies
469
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
joe
▴ 510
7
votes
6
replies
466
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
5 days ago by
analyst
▴ 30
2
votes
5
replies
450
views
Marking duplicates using UMIs
Deduplication
UMI
updated 4 days ago by
i.sudbery
19k • written 5 days ago by
Lipika
• 0
0
votes
6
replies
427
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 2 days ago by
gv
• 0 • written 25 days ago by
Srinka
▴ 20
0
votes
2
replies
420
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
6 days ago by
_quantum_girl_
▴ 10
2
votes
2
replies
418
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 3 days ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
3
votes
9
replies
418
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 2 days ago by
Istvan Albert
100k • written 3 days ago by
Κοσμάς
• 0
1
vote
1
reply
414
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 5 days ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
Chris
▴ 260
4
votes
7
replies
413
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 1 day ago by
dsull
★ 5.8k • written 2 days ago by
VITALA
• 0
1
vote
4
replies
413
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 2 days ago by
atowns21
• 0 • written 5 months ago by
ara
• 0
1
vote
1
reply
403
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
6 days ago by
renan.igor
• 0
194 results • Page
1 of 4
Recent Votes
Comment: genome assembly records not present in assembly_summary.txt
Answer: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: Is there a software that can compare phylogenetic trees to each othe (face to fa
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Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely mapping in regions whe…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
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…
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