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102,916 results • Page
1 of 2059
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STR expansion detection on IonTorrent WES data?
repeat
STR
IonTorrent
wes
ngs
short
tandem
just now by
Joel Wallenius
▴ 90
0
votes
0
replies
1
view
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
just now by
bnayer26
• 0
0
votes
0
replies
5
views
which genome size to use in Fisher's exact test for enrichment?
Fisher
enrichment
1 minute ago by
druggable
▴ 50
1
vote
2
replies
15
views
how to extract columns from csv using a list of name
R
excel
updated 9 minutes ago by
Basti
▴ 480 • written 21 minutes ago by
baijiangshan9726
• 0
0
votes
0
replies
15
views
Job:
Postdoctoral Associate , Baylor College of Medicine, Human Genome Sequencing Center, Houston, United States
TGS
NGS
Job
30 minutes ago by
Medhat
9.3k
0
votes
0
replies
8
views
Job:
Staff Scientist - Bioinformatician, Baylor College of Medicine, Human Genome Sequencing Center, Houston, United States
TGS
NGS
Job
30 minutes ago by
Medhat
9.3k
1
vote
0
replies
13
views
Herald:
The Biostar Herald for Tuesday, June 28, 2022
herald
46 minutes ago by
Biostar
840
0
votes
0
replies
12
views
How to convert CEL file to PLINK format
snp
vcf
plink
apple
cel
47 minutes ago by
Mira
• 0
1
vote
2
replies
33
views
VCF file format | Mandatory information
VCF
fields
Mandatory
updated 1 hour ago by
GenoMax
117k • written 1 hour ago by
its.roops
• 0
0
votes
0
replies
15
views
Gene classification
gene
classification
1 hour ago by
edus_bioinfo
▴ 20
4
votes
2
replies
30
views
why bowtie2 doesn’t report longer than 500bp inserts?
bowtie2
BAM
just now by
lidan0001
▴ 10
0
votes
2
replies
29
views
Efficiently detect Structural Variant
variant
Structural
1 hour ago by
its.roops
• 0
1
vote
2
replies
51
views
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
aspera
ascp
2 hours ago by
ATpoint
62k
6
votes
3
replies
53
views
[R] Same Analysis but different results ?
R
edgeR
GEO
updated 1 hour ago by
Giovanni M Dall'Olio
27k • written 2 hours ago by
ali
▴ 20
0
votes
2
replies
65
views
Bulk RNA-seq with genome but without gene annotation
GFT
wouthou
analysisz
RNA-seq
updated 1 hour ago by
acvill
▴ 100 • written 5 hours ago by
Diego
• 0
5
votes
1
reply
53
views
Using gtf file to get gene positions
gtf
igv
bioinformatics
R
sequencing
updated 3 hours ago by
ahmad mousavi
▴ 670 • written 3 hours ago by
margo
▴ 20
2
votes
2
replies
240
views
Confusion on downloading SRA run data
scrnaseq
runselector
sra
updated 3 hours ago by
vanessagpds
▴ 10 • written 10 days ago by
crx6xw
▴ 10
0
votes
0
replies
26
views
Bimodal read lenghts in pacbio transcriptome sequencing
libraries
pacbio
rna-seq
transcriptome
3 hours ago by
Carlos
• 0
0
votes
1
reply
29
views
Which miRNA arm to select for target prediction, 3p or 5p?
DESeq2
miRNA
Bioinformatics
TargetPredicition
updated 40 minutes ago by
Buffo
★ 1.9k • written 3 hours ago by
Tusharika
• 0
678
votes
160
replies
89k
views
98 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 10 weeks ago by
Biostar
840 • written 5.6 years ago by
Istvan Albert
93k
2
votes
8
replies
160
views
Quick download of FASTQ
aspera
sratoolkit
fastq
updated 2 hours ago by
ATpoint
62k • written 8 hours ago by
Thanh
• 0
1
vote
2
replies
86
views
Less reads are shown using sample_sums() through phyloseq
vegan
Phyloseq
and
2 hours ago by
梓明
▴ 10
0
votes
1
reply
40
views
Bacterial contamination in human DNA sample
Long
read
sequencing
Bacterial
contamination
updated 3 hours ago by
cpad0112
20k • written 4 hours ago by
priya.bmg
▴ 20
0
votes
0
replies
36
views
Linear alignment
Bioinformatics
mapping
alignment
4 hours ago by
Shaima
• 0
3
votes
3
replies
137
views
Extract first and last column of fasta-header
sequence
updated 4 hours ago by
Hugo
▴ 360 • written 19 hours ago by
genomes_and_MGEs
▴ 10
0
votes
1
reply
47
views
RNAseq analysis: I have read counts for all CDS. Could I use standard methods (limma-voom, edgeR) for DEA??
RNAseq
DGE
CDS
mapping
DEA
updated 4 hours ago by
ATpoint
62k • written 5 hours ago by
Elena
• 0
0
votes
0
replies
23
views
the pos in sam file generated by minimap2 can not be correctly parsed.
CIGAR
minimap2
pos
5 hours ago by
Aaron
• 0
2
votes
2
replies
54
views
cram to fastq
cram
fastq
updated 5 hours ago by
ATpoint
62k • written 5 hours ago by
junnna
▴ 10
1
vote
1
reply
175
views
Converting GP field in a VCF to GT
VCF
Threshold
GT
GP
5 hours ago by
Garan
▴ 680
0
votes
0
replies
33
views
Find motif position given a set of enrich peaks
peaks
position
Motif
6 hours ago by
Abdelhamid
• 0
1
vote
0
replies
40
views
News:
Use your standard DNA variant caller for SNP calling in Bisulfite-Seq data
bisulfite
BS-Seq
methylation
6 hours ago by
David Langenberger
9.7k
1
vote
1
reply
71
views
volcano plot display selected labels
volcanoplot
enhancedvolcano
rna-seq
updated 6 hours ago by
Kevin Blighe
81k • written 6 hours ago by
edus_bioinfo
▴ 20
1
vote
3
replies
86
views
R can install .zip package but not .tar.gz package
R
updated 2 hours ago by
Basti
▴ 480 • written 6 hours ago by
Nickier
▴ 20
0
votes
0
replies
41
views
Variant calling from merged bam file with one vcf output
bam
WGS
variant
calling
6 hours ago by
askif4
▴ 10
1
vote
2
replies
73
views
Match genes with the pathway they participate
genes
pathways
databases
updated 3 hours ago by
cpad0112
20k • written 6 hours ago by
eleni.psar
• 0
0
votes
0
replies
27
views
Blog:
Using Transcriptome Sequencing to identify DEGs in response to chemical challenges
Sequencing
RNAseq
Transcriptome
NGS
6 hours ago by
Novogene
▴ 160
0
votes
10
replies
384
views
How to ensure all fonts are written in Arial?
EnhancedVolcano
updated 3 hours ago by
cpad0112
20k • written 4 days ago by
junli1988
• 0
0
votes
0
replies
37
views
Difference between query_alignment_length, template_length, reference_length
pysam
7 hours ago by
tien
• 0
0
votes
0
replies
51
views
How to add to a VCF file's sample information into INFO column?
INFO
loop
VCF
logic
for
updated 8 hours ago by
Pierre Lindenbaum
146k • written 10 hours ago by
wrinklypalms
• 0
0
votes
1
reply
103
views
Why does the CADD database have multiple lines for the same mutation/substitution with different gene IDs?
cadd
updated 9 hours ago by
tomas4482
▴ 140 • written 22 hours ago by
4galaxy77
★ 2.0k
0
votes
1
reply
137
views
How to find DEG within a cluster between two groups without any replication information in scRNA-Seq analysis?
scRNA-Seq
Seurat
Pseudobulk
updated 3 hours ago by
piyushjo
▴ 650 • written 11 hours ago by
Zahra
▴ 50
0
votes
0
replies
84
views
Is there a way to do scRNA seq analysis with Rhapsody (.csv) file using python?
RNA
python
scRNA
analysis
13 hours ago by
Emily
• 0
0
votes
1
reply
112
views
Check if sequence is cytosol-facing?
Topology
Protein
Python
Motif
updated 14 hours ago by
Mensur Dlakic
★ 19k • written 15 hours ago by
ngarber
• 0
0
votes
0
replies
100
views
Replicated samples analysis
repeats
replicates
10 hours ago by
valentinavan
▴ 40
0
votes
0
replies
112
views
Job:
Research Software Engineer, Department of Data Science, Dana-Farber Cancer Institute
engineer
software
17 hours ago by
Laura
• 0
0
votes
1
reply
110
views
How can I parse alternative atom information in a PDB file?
pdb
protein
updated 11 hours ago by
Wayne
★ 1.2k • written 17 hours ago by
user366312
▴ 10
0
votes
7
replies
266
views
can not find certain genes: Ensembl_Gene_Id To Entrezgene using Biomart
gene
R
Biomart
ID
updated 13 hours ago by
GenoMax
117k • written 18 hours ago by
catherine
▴ 210
1
vote
2
replies
221
views
Plink: .vcf to .ped issue (problem with polyploidy?)
polypoidy
Plink
.ped
updated 18 hours ago by
yzliu01
▴ 10 • written 8 weeks ago by
Alice
• 0
0
votes
1
reply
107
views
mRNA contamination in miRNA prep
RIN
miRNA
updated 19 hours ago by
Trivas
▴ 390 • written 1 day ago by
Abhishek
• 0
0
votes
1
reply
105
views
DTU by combining different type of RNA seq data
DTU
analysis
updated 19 hours ago by
Trivas
▴ 390 • written 22 hours ago by
aimanbarki
▴ 20
102,916 results • Page
1 of 2059
Recent Votes
The Biostar Herald for Tuesday, June 28, 2022
why bowtie2 doesn’t report longer than 500bp inserts?
Answer: why bowtie2 doesn’t report longer than 500bp inserts?
Answer: VCF file format | Mandatory information
Answer: Quick download of FASTQ
Answer: why bowtie2 doesn’t report longer than 500bp inserts?
Answer: why bowtie2 doesn’t report longer than 500bp inserts?
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Recent Replies
Comment: how to extract columns from csv using a list of name
by
Basti
▴ 470
Simply use `yourmatrix[,your list]`
Answer: how to extract columns from csv using a list of name
by
caleb_dume
▴ 50
I would recommend looking up the [select][1] function of the dplyr package, convert your matrix to a data frame first. There are many ways …
Comment: Which miRNA arm to select for target prediction, 3p or 5p?
by
Buffo
★ 1.9k
How did you identify those "Differentially expressed miRNAs"?. A single miRNA precursor can originate different mature miRNAs, so, if your …
Comment: Difference in number of DEGs from Deseq2 and limma-voom
by
dzisis1986
▴ 40
I am using a count matrix made after mapping with STAR and quantification with featureCounts. I also filtered the lowly expressed genes bas…
Comment: Network plot from expression data in R using igraph
by
Guido
• 0
Hi Kevin, I was running your excellent, very informative code, but noticed at the end of step 2 a warning; specifically when plotting the t…
Comment: ggscatter, gene expression, correlation
by
Trivas
▴ 390
Two things: 1. You are pivoting your data too early. I generally do this as the last step before plotting. 2. You are better off transposin…
Comment: VCF file format | Mandatory information
by
its.roops
• 0
Thank you..:)
Comment: Efficiently detect Structural Variant
by
its.roops
• 0
It is more or less the same. But, I am looking for some efficient best performing tools that can detect if there is any SV in a very large …
Answer: VCF file format | Mandatory information
by
GenoMax
117k
You must have no doubt seen the specification https://samtools.github.io/hts-specs/VCFv4.3.pdf. Check section starting at `Meta-information…
Comment: Detect Structural Variant
by
Pierre Lindenbaum
146k
how is it different from you previous question: https://www.biostars.org/p/9523381/ ?
Comment: [R] Same Analysis but different results ?
by
Giovanni M Dall'Olio
27k
NP! Your code for subsetting looks correct to me. It makes sense that the differences are not too much. The genes that appear significant i…
Comment: Bulk RNA-seq with genome but without gene annotation
by
acvill
▴ 100
Choice of gene annotation software is going to depend on the organisms you are studying. Eukaryotes? Prokaryotes?
Answer: why bowtie2 doesn’t report longer than 500bp inserts?
by
acvill
▴ 100
By default, bowtie2 expects a maximum fragment length of 500 bp for paired-end alignments. To adjust this, change the `-X` or `--maxins` pa…
Comment: Setting up Aspera Connect (ascp) on Linux and macOS
by
ATpoint
62k
It's not, the release notes say that it was removed on purpose (not saying why though).
Comment: Setting up Aspera Connect (ascp) on Linux and macOS
by
GenoMax
117k
Hopefully this is just a glitch with new version installer and may be fixed by IBM.
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