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90,335 results • Page
1 of 1807
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1
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15
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Batch effect correction of RNA-Seq data
batch-effect
R
RNA-seq
1 hour ago by
Geo
▴ 10
4
votes
6
replies
3.4k
views
Fastqc shows over-represented sequence with no sequence given?
sequencing
updated 1 hour ago by
MboiTui
• 0 • written 5.8 years ago by
chapmansm13
▴ 50
1
vote
1
reply
55
views
how remove large gene ontology terms from gprofiler2 output
gprofiler2
GO
DEseq
RNA-seq
updated 2 hours ago by
jared.andrews07
9.2k • written 11 hours ago by
BISEP
• 0
0
votes
0
replies
15
views
cannot import name 'gcd' from 'fractions'
ubuntu
Linux
python
multiqc
3 hours ago by
h.gaikani
• 0
0
votes
0
replies
17
views
vcftools intersect vs bedtools intersect
bedtools
vcf
vcftools
3 hours ago by
gpen
• 0
0
votes
0
replies
28
views
Job:
R/Shiny web application developer in bioinformatics startup
web
visualization
shiny
3 hours ago by
ivo.kwee
• 0
0
votes
0
replies
23
views
treeProfile out of order
oma
pyham
4 hours ago by
m3hdad
▴ 10
580
votes
155
replies
64k
views
89 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
handbook
tutorial
training
News
updated 1 day ago by
Biostar
10 • written 4.3 years ago by
Istvan Albert
87k
0
votes
0
replies
26
views
Is it bad practice to change threshold for interaction probability?
STRING
Cytoscape
6 hours ago by
gemmalouisebaldock
▴ 10
0
votes
2
replies
458
views
freebayes for snp call in pooled samples: how do I set the parameters?
SNP
freebayes
pooled
ploidy
updated 6 hours ago by
ross_whetten
▴ 10 • written 12 months ago by
cristiana.ij.marques
• 0
0
votes
1
reply
53
views
Can't count features with featurecount
RNAseq
featurecounts
updated 3 hours ago by
Michael Dondrup
48k • written 6 hours ago by
avelarbio46
▴ 10
1
vote
3
replies
105
views
How do I find the gene name with the allele number from the databases?
rna-seq
updated 6 hours ago by
GenoMax
99k • written 10 hours ago by
Rasoulfarzaneh63
• 0
1
vote
1
reply
76
views
How to implement k fold cv after randomForest
k_fold_cv
R
randomForest
updated 5 hours ago by
Mensur Dlakic
★ 10k • written 12 hours ago by
pt.taklifi
▴ 60
4
votes
2
replies
116
views
How to visualize Multiple Sequence Alignment with python ?
python
clustalw
msa
updated 9 hours ago by
Mensur Dlakic
★ 10k • written 15 hours ago by
Junior
• 0
0
votes
0
replies
69
views
Job:
Bioinformatics Laboratory Head, WEHI, Melbourne, Australia
Australia
Job
10 hours ago by
Gordon Smyth
★ 2.5k
0
votes
0
replies
40
views
Quicker way to download gene sequences from NCBI via E-utils
E-utils
NCBI
Gene
Download
Unix
10 hours ago by
lmlukoseviciute
• 0
0
votes
0
replies
46
views
Job:
Postdoc Fellow @ New York City: Alternative Splicing
splicing
genomics
rnaseq
12 hours ago by
fanggang
▴ 100
0
votes
3
replies
118
views
Finding how many times a nucleotide appear in the same position
Beginer
Nucleotide
Python
DNA
updated 8 hours ago by
cpad0112
15k • written 14 hours ago by
ran
• 0
1
vote
2
replies
78
views
Taxonomy assignment of viral RNA
assembly
taxa
metagenomics
11 hours ago by
biobiu
▴ 120
279
votes
54
replies
10k
views
39 follow
Forum:
What Do You Waste Your Time On
bioinformatics
scripting
Forum
updated 13 hours ago by
ponganta
▴ 160 • written 7.9 years ago by
Asaf
8.6k
3
votes
5
replies
149
views
RNAseq data analysis of pooled data
DESeq2
mapping
featurecounts
clustering
RNA-Seq
updated 13 hours ago by
ponganta
▴ 160 • written 20 hours ago by
luffy
• 0
0
votes
0
replies
47
views
Identify sample mix from NGS data
NGS
samplemix
contamination
celllineauthentication
14 hours ago by
Boberoni
• 0
0
votes
0
replies
45
views
CNV-calling single sample
copynumbervariation
cnv
GATK
na12878
15 hours ago by
Boberoni
• 0
0
votes
0
replies
946
views
Is there any Python or other software that can replace the function "networklevel" in R package "bipartite" for calculation?
R
networklevel
16 hours ago by
153348734
• 0
1
vote
1
reply
60
views
GTF file and Transcript ID
transcriptid
rnaseq
gtf
updated 15 hours ago by
GenoMax
99k • written 17 hours ago by
mtavakoli4030
• 0
0
votes
0
replies
30
views
Couldnot access BSRD database
database
website
BSRD
17 hours ago by
madhujamano
• 0
0
votes
0
replies
42
views
CPM or TPM values as discretization method input
RNA-Seq
discretization
TPM
CPM
15 hours ago by
antmantras
• 0
2
votes
1
reply
67
views
How to extract all columns of CSQ using split-vep plugin of bcftools?
plugin
samtools
bcftools
vcf
split-vep
updated 15 hours ago by
Pierre Lindenbaum
135k • written 18 hours ago by
dare_devil
★ 1.4k
3
votes
4
replies
157
views
Expression of gene of interest across conditions in single-cell data
singlecell
scater
tpm
seurat
Rna-seq
1 hour ago by
kz
• 0
0
votes
1
reply
102
views
bbmap, mapq and uniquelly mapped reads filtering
alignment
mapq
updated 1 day ago by
GenoMax
99k • written 1 day ago by
boczniak767
▴ 740
0
votes
2
replies
153
views
Cell composition in each condition of single cell data
cell
composition
single-cell
scProportionTest
22 hours ago by
paria.alipour
▴ 20
2
votes
6
replies
200
views
Generate a file with SNPs given a WGS dataset
annotation
snp
ngs
3 hours ago by
iibrams07
• 0
0
votes
0
replies
75
views
Calculate relative position of one range with respect to another
Bioconductor
IRanges
GenomicRanges
R
1 day ago by
Andrew
• 0
0
votes
5
replies
256
views
Limma experiment design and making contrasts
limma
methylation
450k
1 day ago by
kra277
• 0
1
vote
3
replies
335
views
Keep values from VCF file into Ensembl VEP annotation
SNP
updated 19 hours ago by
dare_devil
★ 1.4k • written 3 months ago by
brunobsouzaa
▴ 520
4
votes
6
replies
259
views
Using outgroup in gene family dendograms
mega
dendograms
9 hours ago by
Rogerio Ribeiro
▴ 50
0
votes
0
replies
83
views
I can not get fasta file with the hit sequences running barrnap
barrnap
bed
updated 1 day ago by
Ram
32k • written 1 day ago by
pavelasquezv
▴ 10
0
votes
1
reply
83
views
Raw read processing using trimmomatic
trimmomatic
updated 1 day ago by
boczniak767
▴ 740 • written 1 day ago by
CHINMAYA
• 0
14
votes
9
replies
289
views
How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
transcript
rna-seq
3 hours ago by
Quanyou
• 0
0
votes
2
replies
150
views
MASURCA error for multiple entries
masurca
1 day ago by
kilcdincer
• 0
2
votes
3
replies
154
views
How to extract only the specific fasta sequences by matching the ID's to a different source files ?
RNA
alignment
DNA
updated 8 hours ago by
Prakash
★ 2.1k • written 1 day ago by
pinn
▴ 90
2
votes
2
replies
92
views
Download discontinued gene record from NCBI via E-utils
E-utils
NCBI
Discondinued
Gene
16 hours ago by
lmlukoseviciute
• 0
4
votes
6
replies
242
views
Creating reference genome for mapping and then selecting
mm10
hg38
STAR
RNA-seq
updated 1 day ago by
Istvan Albert
87k • written 1 day ago by
Dataminer
★ 2.7k
0
votes
2
replies
162
views
ExomeDepth negative BF (bayesian factor) values meaning
WES
DNA-seq
CNV
updated 1 day ago by
German.M.Demidov
★ 2.0k • written 9 weeks ago by
John
▴ 160
2
votes
1
reply
77
views
Tool to find chromosome specific repeats
FISH
repeats
transposons
genomics
updated 1 day ago by
Michael Dondrup
48k • written 1 day ago by
giova34
• 0
0
votes
1
reply
69
views
Different results in limma if group is removed
limma
edgeR
updated 1 day ago by
Kevin Blighe
72k • written 1 day ago by
Palgrave
▴ 20
0
votes
0
replies
36
views
LOOCV on limma results
loocv
limma
cross-validation
updated 1 day ago by
ATpoint
47k • written 1 day ago by
Palgrave
▴ 20
0
votes
1
reply
67
views
About combining the forward and reverse sequence
16srRNA
geneious
updated 1 day ago by
Istvan Albert
87k • written 1 day ago by
ruddhida
• 0
0
votes
0
replies
38
views
mtDNA variant calling
variant
fasta
seq
mtdna
1 hour ago by
here_for_learning
• 0
0
votes
1
reply
95
views
How can I revert back the ensemble vep annotated positions to vcf positions?
VCF
ensembl
VEP
updated 1 day ago by
finswimmer
14k • written 1 day ago by
dare_devil
★ 1.4k
90,335 results • Page
1 of 1807
Recent Votes
Batch effect correction of RNA-Seq data
Answer: how remove large gene ontology terms from gprofiler2 output
Answer: How to implement k fold cv after randomForest
Comment: Expression of gene of interest across conditions in single-cell data
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Answer: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
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Comment: how to run CD-Search with python or biopython
by
johnny.sf
▴ 10
You can use a module called Selenium in Python to access CD Search. From there, it is just a way to find the elements that you want. For …
Comment: Expression of gene of interest across conditions in single-cell data
by
kz
• 0
Figured it out, thank you!!
Answer: Fastqc shows over-represented sequence with no sequence given?
by
MboiTui
• 0
This is the result of not removing sequences with 0 length after trimming (hence why it is not reporting the base pairs). Set the minimum s…
Answer: how remove large gene ontology terms from gprofiler2 output
by
jared.andrews07
9.2k
You could limit based on the `term_size`, filtering terms from the results that have a ton of associated genes and tend to be less interest…
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
by
Quanyou
• 0
This might be the most reasonable solution. Thanks a lot.
Comment: Generate a file with SNPs given a WGS dataset
by
iibrams07
• 0
By code I mean the command line code needed to run the pipeline and not to download GATK. Clicking at best practices workflow, one is led …
Comment: Can't count features with featurecount
by
Michael Dondrup
48k
Some issues: - do a qc on your alignments with the output from star and bamtools stats or similar. How many of your alignments are in fa…
Comment: Generate a file with SNPs given a WGS dataset
by
Dave Carlson
▴ 610
SNP = single nucleotide polymorphism SNV = single nucleotide variant These two things are subtlety different, but they are not totally di…
Comment: Generate a file with SNPs given a WGS dataset
by
iibrams07
• 0
The samples the DNA was extracted from were somatic cells. It is surprising that GATK provides more pipelines for germ cells than somatic o…
Comment: How do I compare degree and betweenness centrality for different PPI networks?
by
gemmalouisebaldock
▴ 10
Thank you very much, Istvan, I believe I have found a way to rectify this issue.
Comment: Expression of gene of interest across conditions in single-cell data
by
jared.andrews07
9.2k
Does it spit out an error message? That should work, but you can also [open an issue on the Github](https://github.com/dtm2451/dittoSeq/iss…
Answer: freebayes for snp call in pooled samples: how do I set the parameters?
by
ross_whetten
▴ 10
According to the [Freebayes documentation][1], with the --pooled-continuous option " When running with high --ploidy settings, it may be re…
Comment: Generate a file with SNPs given a WGS dataset
by
Dave Carlson
▴ 610
To exclude all but SNPs from your VCF file you can use GATK's SelecVariants tool with `--select-type-to-include SNP` or bcftools with `--sk…
Comment: How do I find the gene name with the allele number from the databases?
by
GenoMax
99k
I don't immediately see a connection between the two examples you provided. What is `X_84670461` and how is it related to `26_23089878 `? W…
Comment: Generate a file with SNPs given a WGS dataset
by
iibrams07
• 0
@Dave Carlson. Many thanks. Once at step 6., what should I do to collect only the SNPs and discard other variants? I need to pipe this coll…
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