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130 results • Page
1 of 3
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Views
Votes
Replies
3
votes
12
replies
2.2k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 5 days ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
1
vote
9
replies
321
views
Trying to edit VCF file
VCF
R
bcftools
snpsaurus
updated 1 day ago by
Ram
39k • written 1 day ago by
peavy
• 0
0
votes
8
replies
348
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 5 days ago by
GenoMax
129k • written 6 days ago by
Marta
• 0
4
votes
8
replies
1.6k
views
How to extract promoter sequences from a plant draft genome?
promoter
genome
updated 4 days ago by
Ram
39k • written 3.7 years ago by
Kumar
▴ 100
0
votes
8
replies
1.5k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython
python
updated 21 hours ago by
Ram
39k • written 3.5 years ago by
muhammad.khizerkiet
• 0
4
votes
7
replies
2.2k
views
low bootstrap value?
phylogeny
genome
alignment
updated 6 days ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
3
votes
7
replies
1.1k
views
Find 3'UTRs for species
Assembly
alignment
updated 4 days ago by
Ram
39k • written 3.8 years ago by
Palgrave
▴ 110
2
votes
6
replies
646
views
How to identify the corresponding gene of a short sequence of a genome?
fasta
gene
genome
sequence
updated 20 hours ago by
Ram
39k • written 3.5 years ago by
Kumar
▴ 100
0
votes
6
replies
331
views
variant allelic fraction
vep
updated 21 hours ago by
Ram
39k • written 2 days ago by
Jom
• 0
4
votes
6
replies
1.5k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 5 days ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
2
votes
5
replies
291
views
Embryo transcriptome
database
transcriptome
SRA
updated 1 day ago by
ATpoint
72k • written 1 day ago by
firefox91
• 0
0
votes
5
replies
389
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 4 days ago by
Joe
21k • written 5 days ago by
gunala.nikhil
• 0
0
votes
4
replies
367
views
What are recommended parameters for the local protein alignment ?
protein
alignment
3 days ago by
Alexander
▴ 70
2
votes
4
replies
823
views
Downloading all the heteroComplex protein PDB IDs in RCSB Protein Data Bank
python
biopython
updated 1 day ago by
Ram
39k • written 3.6 years ago by
Christian
• 0
0
votes
4
replies
652
views
Error in PGAP pangenome pipeline?
sequence
genome
sequencing
gene
updated 19 hours ago by
Ram
39k • written 3.5 years ago by
Kumar
▴ 100
1
vote
4
replies
225
views
Is hg38 on the multiz 30-way alignment inaccurate?
maf
UCSC
PHAST
multiz
1 day ago by
Daniel
▴ 30
2
votes
4
replies
239
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 6 days ago by
Ram
39k • written 6 days ago by
miguellarrazlopezdenovales
• 0
0
votes
4
replies
201
views
Difference between USCS exon coordinates and ensembl
exons
Ensembl
1 day ago by
amy__
▴ 50
0
votes
4
replies
279
views
Identification of genes involved in my pathway
KEGG
keggGet
5 days ago by
smanzano250800
• 0
0
votes
4
replies
5.0k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 1 day ago by
Franco
• 0 • written 5.6 years ago by
ac.research
▴ 30
4
votes
4
replies
293
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 5 days ago by
ATpoint
72k • written 5 days ago by
bioinfo
▴ 80
0
votes
3
replies
2.4k
views
Generate GTF/GFF file (coordinates) from a FASTA annotated file.
Assembly
genome
updated 4 days ago by
Ram
39k • written 3.7 years ago by
marquezg48
• 0
1
vote
3
replies
598
views
What is the best approach to detect unknown recombinant gene in genome?
recombinant
sequencing
updated 19 hours ago by
Ram
39k • written 3.4 years ago by
Can Holyavkin
▴ 240
1
vote
3
replies
201
views
Differential protein expression analysis
R
proteomic
statistics
updated 1 hour ago by
dsull
★ 4.2k • written 3 days ago by
Ribo
▴ 40
1
vote
3
replies
190
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 6 days ago by
Pierre Lindenbaum
154k • written 7 days ago by
herh
• 0
1
vote
3
replies
221
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 6 days ago by
GenoMax
129k • written 6 days ago by
mls
• 0
0
votes
3
replies
218
views
Gviz Coverage Plots
gviz
scrnaseq
cellranger
r
updated 14 hours ago by
Ram
39k • written 19 hours ago by
Researcher
• 0
1
vote
3
replies
72
views
Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
RNA-evidence
genome
prediction
masking
updated 49 minutes ago by
Darked89
4.4k • written 3 hours ago by
Ayish
• 0
0
votes
3
replies
227
views
hardfilter error
bam
recall
5 days ago by
bestone
▴ 10
3
votes
3
replies
190
views
retaining only the clusters of interest
seurat
single-cell
scRna-seq
updated 8 hours ago by
rfran010
▴ 160 • written 17 hours ago by
shamza
• 0
2
votes
3
replies
213
views
Same GEO Accession, different SRR number, how to download this RNA-seq paired-end data?
sra-toolkit
fastq
RNA-seq
SRA
updated 22 hours ago by
GenoMax
129k • written 23 hours ago by
ev97
• 0
0
votes
3
replies
180
views
DEGseq for multiple samples
DEGseq
DEG
updated 5 days ago by
Ram
39k • written 6 days ago by
ALOUSH ALI
• 0
2
votes
3
replies
341
views
Low mapping percentage
mapping
STAR
RNAseq
3 days ago by
Sib
▴ 40
0
votes
3
replies
721
views
How can I use KING on windows ?
plink
king
updated 6 days ago by
Ram
39k • written 4.1 years ago by
gwas_maniac
▴ 20
2
votes
3
replies
1.2k
views
mutational signatures in different tumor samples
somatic mutation
mutational signature
updated 5 days ago by
Vincent Laufer
★ 2.9k • written 4.4 years ago by
lzy
▴ 20
0
votes
3
replies
322
views
(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
bowtie2
align_stats
trinity
2 days ago by
eimanpharmacist
▴ 20
0
votes
3
replies
196
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
6 days ago by
Mohd
▴ 20
0
votes
3
replies
210
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 6 days ago by
andres.firrincieli
3.4k • written 7 days ago by
kamanovae
▴ 80
1
vote
3
replies
1.4k
views
Is there any tool available for sequence alignment concatenation and supermatrix file generation other than Fastconcat-G?
Assembly
alignment
software-error
updated 1 day ago by
Ram
39k • written 3.6 years ago by
Kumar
▴ 100
1
vote
3
replies
210
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 5 days ago by
GenoMax
129k • written 6 days ago by
NikhilP
▴ 20
1
vote
3
replies
182
views
Obtain a --gene-trans-map file after rnaSPAdes
rnaSPAdes
Trinity
1 day ago by
UserA
• 0
1
vote
2
replies
176
views
hisat2 Error 137
hisat2
RNA-seq
1 day ago by
Forough
▴ 10
0
votes
2
replies
167
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
6 days ago by
survive
• 0
0
votes
2
replies
224
views
Diff Bind Questions
DiffBind
CHiP-Seq
updated 18 hours ago by
Ram
39k • written 1 day ago by
B.N.
• 0
1
vote
2
replies
209
views
Combination of ROC CURVE
roccurve
R
AUC
2 days ago by
Maria17
▴ 20
0
votes
2
replies
520
views
1-way-2-fold cross family analysis
cross-family-analysis
updated 6 days ago by
Ram
39k • written 3.8 years ago by
sinha.shriprakash
▴ 20
0
votes
2
replies
301
views
too many zeros in 16S rRNA amplicon sequencing data
16S
rRNA
23 hours ago by
zhangdengwei
▴ 190
0
votes
2
replies
22
views
How to use R installed by conda instead of it installed by apt on Ubuntu
R
ubuntu
conda
23 minutes ago by
Zhichao
• 0
2
votes
2
replies
182
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
analysis
CD
Protocol
updated 20 hours ago by
Ram
39k • written 6 days ago by
linnet.roque6
▴ 10
0
votes
2
replies
1.0k
views
Find most upregulated genes in one library?
EdgeR
RNA-Seq
Rsubread
updated 1 day ago by
Ram
39k • written 3.7 years ago by
williams.damon26
▴ 10
130 results • Page
1 of 3
Recent Votes
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
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Recent Replies
Comment: switching from illumination to NEB prep kits
by
GenoMax
129k
If you are simply replacing the library prep kit then it will be compatible with normal illumina libraries. If there is a different adapter…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
Zhichao
• 0
yes, I have activated this conda environment. And the conda is in `PATH` . At first, I create a new conda environment `conda create -n ne…
Comment: Limma returned only positive logFC values
by
ATpoint
72k
Raw counts, raw meaning not manipulated by any transformation. See limma and edgeR manual, it clearly covers that for using limma-trend and…
Comment: Alternative To interactions comparison in limma in DESeq2
by
ATpoint
72k
https://support.bioconductor.org/p/9143932/ -- see the lower parts where Michael Love answers, it comes down to numeric contrasts.
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
The `mat` is log2-normalized raw data. Is it feasible? Or should I feed in counts?
Comment: DESeq2 for different design and normalized counts
by
ATpoint
72k
Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
ATpoint
72k
Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
Comment: Limma returned only positive logFC values
by
ATpoint
72k
Bottom line is, if you are using an intercept-free model (that is what `~0+...` is doing) then you have to use contrasts. In a "normal" mod…
Comment: Asking for feedback on a Python library for computing alignments
by
Alexander
▴ 70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Darked89
4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
Thanks a lot, it works
Comment: Differential protein expression analysis
by
dsull
★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
Comment: Differential protein expression analysis
by
Ribo
▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
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