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478 results • Page
1 of 10
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2
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1
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30
views
How to merge unique/non overlapping genes between 2 gene model GFF3 files?
gff3
updated 28 minutes ago by
jv
▴ 780 • written 3 hours ago by
William
★ 5.1k
0
votes
0
replies
23
views
Unrooted consensus tree [Bio.Phylo]
consensus
phylo
biopython
1 hour ago by
Jimpix
▴ 10
0
votes
0
replies
19
views
PLINK2 selecting variants based on INFO score
plink2
2 hours ago by
m.c.roozen
• 0
0
votes
3
replies
69
views
DESeq2 results function runs very slow on Windows 10
r
deseq2
updated 46 minutes ago by
ATpoint
68k • written 2 hours ago by
Taha
• 0
0
votes
2
replies
67
views
How can I convert this pairwise format to fasta?
fasta
python
bash
updated 1 hour ago by
Ram
37k • written 3 hours ago by
SaltedPork
▴ 170
0
votes
2
replies
136
views
Trimmomatic
Trimmomatic
RNA
quality-check
updated 1 hour ago by
Ram
37k • written 19 hours ago by
Monia
• 0
0
votes
0
replies
27
views
What is the difference between gseapy.prerank and gseapy.gsea?
gseapy
gsea
3 hours ago by
bioinfo
▴ 20
1
vote
2
replies
86
views
When you convert a BAM back into a FastQ do you get the original Fastq?
bam
FastQ
updated 3 hours ago by
GenoMax
125k • written 5 hours ago by
louis-gil
• 0
3
votes
6
replies
112
views
Which file and data structure is used to create volcano plot from scRNA-Seq experiment?
plot
Volcano
1 hour ago by
Chris
▴ 60
0
votes
1
reply
51
views
Converting large GSM from GEOquery into a minfi or limma workable set
minfi
methylation
limma
GEOquery
R
updated 3 hours ago by
Basti
★ 1.3k • written 4 hours ago by
Edward E-B
• 0
1
vote
1
reply
59
views
bwa mem duration?
performance
mapping
bwa
updated 4 hours ago by
ATpoint
68k • written 4 hours ago by
lacb
▴ 30
8
votes
9
replies
2.5k
views
7 follow
Translating gene names to entrez id's
database
annotation
biopython
gene
python
updated 3 hours ago by
Ram
37k • written 22 months ago by
Julian
• 0
0
votes
1
reply
85
views
Gene ontology with locus tags
ontology
locus
gene
tags
updated 3 hours ago by
dthorbur
▴ 260 • written 6 hours ago by
sea.joson
▴ 10
3
votes
2
replies
171
views
High downstream gene expression
downstream
High
Gene
expression
updated 7 hours ago by
i.sudbery
16k • written 12 hours ago by
yoser4
▴ 10
0
votes
1
reply
86
views
Clustering and dynamic tree cutting
dynamicTreeCut
Clustering
data
RNAseq
cutreeDynamic
updated 5 hours ago by
andres.firrincieli
3.1k • written 7 hours ago by
harish
• 0
0
votes
6
replies
192
views
STAR is running but .sam file size does not increase after hours mapping
STAR
RNA-seq
mapping
SAM
updated 5 hours ago by
GenoMax
125k • written 7 hours ago by
luzglongoria
▴ 40
2
votes
2
replies
157
views
Annotating ENS codes to gene name
expression
RNA-seq
DEseq2
updated 7 hours ago by
GenoMax
125k • written 10 hours ago by
yoosefyud
▴ 40
0
votes
4
replies
175
views
HTSeq error processing GFF file
HTSeq
GFF
GTF
1 hour ago by
ibq.enriquepola
• 0
0
votes
0
replies
70
views
which tool to use for Transposon structure finding CENSOR or repeat masker ??
transposon
DNA
repeat
CENSOR
masker
14 hours ago by
manaswiniparija3
▴ 10
0
votes
1
reply
123
views
Using Entrez Utilities to query the Nucleotide database by collection_date
ncbi
entrez
updated 16 hours ago by
GenoMax
125k • written 16 hours ago by
anomalous.lexeme
• 0
0
votes
0
replies
70
views
scATAC merging of files
Signac
scATAC-seq
17 hours ago by
bioinformatics.girl
• 0
0
votes
1
reply
139
views
Manual Polygenic Risk Score calculation
calculation
steps
PRS
updated 17 hours ago by
Sam
★ 4.6k • written 1 day ago by
Roy
▴ 10
4
votes
4
replies
292
views
2D structure of a custom protein (not in any databases) from a PDB file.
Tool
Pymol
PDB
protein
structure
updated 18 hours ago by
Jiyao Wang
▴ 290 • written 2 days ago by
Hansen_869
▴ 50
0
votes
0
replies
84
views
what does ALT ID DUP refer to when ALT ID for copy number are already specified
ALT
ID
CNV
VCF
19 hours ago by
anubratadas
▴ 20
0
votes
0
replies
105
views
How to use gseapy after scanpy?
gsea
single
cell
enrichR
gseapy
3 hours ago by
bioinfo
▴ 20
0
votes
0
replies
89
views
VNTR genotyping
NGS
VNTR
genotyping
20 hours ago by
Genotepes
▴ 950
0
votes
0
replies
83
views
Which AF column do I use from TCGA data in maftools
vcf2maf
sequencing
genome
WES
maf
21 hours ago by
CH1374
▴ 10
0
votes
3
replies
189
views
Faking hh-suite workflow / alignment output
alignment
hhsuite
updated 17 hours ago by
Mensur Dlakic
★ 22k • written 22 hours ago by
Nick
▴ 40
0
votes
4
replies
256
views
RNASeq differential expression masked by pathways disregulation
normalization
Rnaseq
batch
updated 7 hours ago by
i.sudbery
16k • written 1 day ago by
Gama313
▴ 110
0
votes
0
replies
80
views
Chloroplast genome phylogenetic analysis
Inverted
region
Chloroplast
genome
Phylogenetic
analysis
SSC
21 hours ago by
a.bibek52
• 0
0
votes
0
replies
78
views
mVISTA annotation
alignment
Annotation
S-LAGAN
mVISTA
21 hours ago by
a.bibek52
• 0
0
votes
1
reply
139
views
Create a new seurat object using one cluster identified in a previous seurat object
object
seurat
Create
clusterization
updated 21 hours ago by
Ribo
▴ 20 • written 1 day ago by
Fernanda
• 0
2
votes
2
replies
164
views
Analyzing bulk RNA-seq
RNAseq
updated 20 hours ago by
swbarnes2
13k • written 23 hours ago by
Zaid
• 0
0
votes
5
replies
190
views
Why am I getting only one common value when comparing two excel files?
python
pandas
excel
updated 23 hours ago by
seidel
10k • written 1 day ago by
namck
• 0
2
votes
4
replies
183
views
Alien-hunter outputs
alien-hunter
51 minutes ago by
schlogl
▴ 130
1
vote
13
replies
303
views
RNAseq for DE purpose
RNAseq
updated 20 hours ago by
swbarnes2
13k • written 23 hours ago by
m.habib
• 0
0
votes
0
replies
73
views
Identifying off-target mutation frequency in Bacterial genomes
dCas9-deaminase
off-target
SNPS
WGS
dCas9
1 day ago by
pd378
• 0
1
vote
3
replies
225
views
Simulating metatranscriptomic shotgun reads
metatranscriptomic
RNA
simulated-reads
shotgun-sequencing
updated 1 day ago by
Mensur Dlakic
★ 22k • written 2 days ago by
sovrappensiero
▴ 50
0
votes
0
replies
69
views
News:
Eukaryotic Metabarcoding course
eDNA
Metabarcoding
updated 23 hours ago by
Ram
37k • written 1 day ago by
carlopecoraro2
★ 2.2k
1
vote
1
reply
112
views
want the codes for Deseq2 to perform DEGs.
DEGs
updated 1 day ago by
ATpoint
68k • written 1 day ago by
rupali
• 0
0
votes
0
replies
69
views
SVA correction reduces ability to detect genes as differential expressed?
effects
RNAseq
expression
batch
SVA
gene
1 day ago by
MB
▴ 50
0
votes
7
replies
302
views
CoveragePlot in Signac from MACS2 Object
Signac
scATAC-seq
updated 3 hours ago by
seidel
10k • written 1 day ago by
bioinformatics.girl
• 0
0
votes
1
reply
104
views
Looking for RNA-seq aligner that can identify not properly mapped paired
aligner
paire-end
rna-seq
updated 1 day ago by
Matthias Zepper
2.9k • written 1 day ago by
romain.lannes
▴ 90
0
votes
2
replies
113
views
News:
NCBI update complete. Aspera users please update your client.
NCBI
Submissions
GenBank
1 day ago by
PeterC_NCBI
▴ 180
0
votes
1
reply
117
views
Remove duplicates in multifasta, where entries are paired
bash
python
updated 3 hours ago by
dthorbur
▴ 260 • written 1 day ago by
SaltedPork
▴ 170
1
vote
3
replies
151
views
'SyntaxError': 'return' outside function?
biopython
pattern
python
regex
updated 23 hours ago by
GenoMax
125k • written 1 day ago by
namck
• 0
1
vote
1
reply
113
views
snakemake Unexpected keyword bam in rule definition
snakemake
updated 1 day ago by
Ram
37k • written 1 day ago by
Aidand
• 0
0
votes
1
reply
122
views
How to remove from BAM file header all chromosomes, except chrM
samtools
header
updated 1 day ago by
Pierre Lindenbaum
152k • written 1 day ago by
User000
▴ 620
0
votes
0
replies
74
views
Normalize Together Total RNA-SEQ vs Ampliseq protocols reads
RNA-seq
deseq2
ampliseq
ion-torrent
R
1 day ago by
Fernando
• 0
0
votes
0
replies
78
views
Combining mRNA and total RNA studies
RNA-Seq
bulk
updated 1 day ago by
Ram
37k • written 1 day ago by
aksh
• 0
478 results • Page
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Recent Votes
Answer: Multiple sequence alignment of sequenecs of different length
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Comment: Alien-hunter outputs
Answer: Annotating ENS codes to gene name
Comment: Annotating ENS codes to gene name
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe
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Recent Replies
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
by
jv
▴ 780
`bedtools intersect -v` is one option for identifying the unique genes from the older gene model. <https://bedtools.readthedocs.io/en/lates…
Comment: Alien-hunter outputs
by
schlogl
▴ 130
@GenoMax Hope this helps...Thank you
Comment: DESeq2 results function runs very slow on Windows 10
by
ATpoint
68k
Does it go away if you remove the `parallel` from `results()`? After all, it is the `DESeq()` function that is the bottleneck when n is lar…
Comment: HTSeq error processing GFF file
by
ibq.enriquepola
• 0
enrique@L:~/bioinformatica/index/prueba$ head -n 997531 GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.gff|tail -n 1 NC_007982.1 Ref…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe
by
Chris
▴ 60
Thank you for your help! I got an error that I could not find the solution on the Internet: library(EnhancedVolcano) Loading required…
Comment: HTSeq error processing GFF file
by
barslmn
★ 1.2k
I guess you can try to replace the "?" to a "." Also, you can copy and paste text instead of the screenshots?
Answer: DESeq2 results function runs very slow on Windows 10
by
Istvan Albert
96k
Note the following: https://support.bioconductor.org/p/115415/ it looks like it has to do with the Parallel=TRUE flag
Comment: DESeq2 results function runs very slow on Windows 10
by
GenoMax
125k
> there is a massive difference in performance between them. It still is taking only one minute.
Comment: HTSeq error processing GFF file
by
ibq.enriquepola
• 0
Yes, ![enter image description here][1] [1]: /media/images/76ecd9a7-10c2-4526-9849-062605ca
Answer: How can I convert this pairwise format to fasta?
by
GenoMax
125k
This seems to be the output from `sam2pairwise` program: https://github.com/mlafave/sam2pairwise A dirty way may be $ grep -A 1 ^M039…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe
by
Basti
★ 1.3k
EnhancedVolcano(CV.markers, x = "avg_log2FC", y = "p_val", lab = rownames(CV.markers), pCutoff = 1e-4, FCcutoff =…
Comment: How to perform multiple comparisons using edgeR?
by
ryandward
• 0
Actually, you get one FDR per gene if you don't loop, and perform the comparisons all at once.
Comment: Remove duplicates in multifasta, where entries are paired
by
dthorbur
▴ 260
I don't have an existing tool that would do it, but if your fasta files aren't that large, it would be quite easy to do in R. You could cre…
Comment: How can I convert this pairwise format to fasta?
by
Shred
▴ 990
It's a SAM file. https://samtools.github.io/hts-specs/SAMv1.pdf For conversion https://www.biostars.org/p/129763/
Comment: Translating gene names to entrez id's
by
Ram
37k
While you're doing what @genomax says, please avoid `<pre><code>`. Use markdown (or the editor toolbar) instead.
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