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1,000 results • Page
1 of 20
Sort: Rank
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0
votes
0
replies
6
views
How to compare two sequence logo?
bioinformatics
4 minutes ago by
Andrew Liu
▴ 10
0
votes
2
replies
52
views
Clustered, annotated dotplot to scRNA-Seq data
scRNA-Seq
dotplot
visualization
updated just now by
Friederike
8.4k • written 3 hours ago by
tomer9w
• 0
0
votes
0
replies
5
views
Snakemake cluster execution error
cluster
snakemake
conda
20 minutes ago by
blackadder
• 0
0
votes
1
reply
10
views
doubts about SNAP, bioinformatic tools for gene prediction
gene
prediction
updated just now by
lieven.sterck
14k • written 24 minutes ago by
JUAN LUIS
• 0
0
votes
1
reply
88
views
Computationally generated transcriptional regulation network
GRN
updated 38 minutes ago by
Matthias Zepper
▴ 910 • written 12 hours ago by
nicoyanovsky
• 0
0
votes
1
reply
31
views
Forum:
Getting the best of RNA-Seq
RNA-Seq
isoform
gene
expression
updated 28 minutes ago by
ATpoint
62k • written 49 minutes ago by
Antonio R. Franco
★ 4.8k
0
votes
0
replies
10
views
News:
online training - Data Visualization with Python
Visualization
Python
Data
48 minutes ago by
carlopecoraro2
★ 2.1k
0
votes
1
reply
136
views
How to count the number of multimapped reads from a bam file?
rnaseq
mapping
bowtie2
featurecounts
updated 59 minutes ago by
Shred
▴ 640 • written 2 days ago by
O.rka
▴ 600
0
votes
2
replies
41
views
How to find average read length and number of reads in a bam file using samtools in linux?
bam
sequencing
read
samtools
20 minutes ago by
MobiusT
• 0
1
vote
2
replies
38
views
Tool similar to CollectGcBiasMetrics
metrics
picards
bioinformatics
gcbias
tool
43 minutes ago by
tea.vuki
▴ 10
0
votes
3
replies
80
views
Align short sequence against ONT reads
reads
ONT
long
genome
alignment
updated just now by
Friederike
8.4k • written 6 hours ago by
kirillkirilenko.tomsk
• 0
0
votes
0
replies
36
views
Gene ontology enrichment vs. REACTOME pathway analysis
GO
REACTOME
4 hours ago by
Gene_MMP8
▴ 210
0
votes
0
replies
31
views
News:
Cellosaurus release 42 is available
line
cell
biocuration
knowledgebase
database
4 hours ago by
Amos Bairoch
▴ 110
0
votes
0
replies
31
views
mRNA contamination in miRNA prep
RIN
miRNA
4 hours ago by
Abhishek
• 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
830 • written 5.6 years ago by
Istvan Albert
93k
0
votes
0
replies
28
views
extract rRNA/tRNA and other ncRNA ratio in a table from small RNA-seq
non-coding
small
RNA-seq
miRNA
analysis
RNA
clustering
5 hours ago by
Rey
• 0
0
votes
0
replies
36
views
TCGA CIMP status
Bioinformatics
TCGA
COAD
6 hours ago by
ilomilo
• 0
0
votes
1
reply
73
views
Question regarding normalization in Seurat
Seurat
scRNAseq
updated 2 hours ago by
ATpoint
62k • written 6 hours ago by
ylin575
▴ 10
0
votes
0
replies
66
views
PCA and logistic regression in GWAS
logistic
GWAS
PCA
regression
12 hours ago by
gosssheen
• 0
0
votes
2
replies
88
views
PCA plot for miRNA
miRNA
PCA
3 hours ago by
struggler
• 0
0
votes
6
replies
162
views
Ribosomal Depletion
rRNA
STAR
sequencing
contamination
RNA
updated 13 hours ago by
andres.firrincieli
★ 2.5k • written 15 hours ago by
kcarery
• 0
0
votes
1
reply
111
views
Error with TCGA package - TCGAbiolinks
TCGA
r
cancer
updated 10 hours ago by
Kevin Blighe
81k • written 19 hours ago by
JACKY
▴ 10
0
votes
0
replies
58
views
Question about rMATS output files
rMATS
novel
19 hours ago by
Lillian
• 0
1
vote
6
replies
298
views
ESTIMATE tumor purity
purity
r
cancer
19 hours ago by
JACKY
▴ 10
1
vote
6
replies
210
views
Exctract unmapped reads from BLAST
blatella
unmapped
germanica
annotation
blast
trinotate
16 hours ago by
Pilar
• 0
4
votes
3
replies
4.5k
views
Resfams Database usage
Resfams
updated 22 hours ago by
Neel
▴ 10 • written 6.1 years ago by
ginna
▴ 10
0
votes
1
reply
79
views
Searching for RNA-seq melanoma samples in TCGA or cBioPortal
TCGA
r
cBioPortal
cancer
updated just now by
Friederike
8.4k • written 1 day ago by
JACKY
▴ 10
0
votes
1
reply
286
views
Quast Ouput
Contig
Quast
updated 1 day ago by
Ying
• 0 • written 9 months ago by
kishorssf91
• 0
0
votes
1
reply
150
views
SRA obtained metagenomic reads appears to corrupt - cannot work on SingleM
SingleM
SRAtoolkit
updated 20 hours ago by
GenoMax
117k • written 1 day ago by
rfour92
• 0
0
votes
1
reply
208
views
Get nucleotide sequence of assembled RNA transcripts
transcript
assembly
RNA-seq
chimeric
RNA
updated 1 day ago by
tomas4482
▴ 140 • written 12 days ago by
drabiza1
▴ 10
1
vote
0
replies
129
views
gene strand determined by flag in read1 and read2 should be intepreted differently?
bam
flag
samtools
RNA-seq
1 day ago by
tomas4482
▴ 140
0
votes
1
reply
159
views
Error in downloading scRNA data from ENA with wget
scRNA
updated 1 day ago by
GenoMax
117k • written 1 day ago by
Aryan
• 0
0
votes
0
replies
123
views
Estimating gene family size changes for a large tree?
Phylogenetics
CAFE5
1 day ago by
Rijan
▴ 30
1
vote
2
replies
205
views
Quick way to get a field such as QNAME from the last read in a bam file?
bam
samtools
1 day ago by
kalavattam
▴ 70
1
vote
1
reply
251
views
Fast way to sort bam file by queryname similar to picard SortSam SORT_ORDER=queryname?
bam
picard
sort
samtools
updated 1 day ago by
Pierre Lindenbaum
146k • written 2 days ago by
kalavattam
▴ 70
0
votes
1
reply
122
views
converting a DocumentTermMatrix to factor
DocumentTermMatrix
convert
factor
offtopic
updated 1 day ago by
cpad0112
20k • written 2 days ago by
hasani.iut6
▴ 70
0
votes
0
replies
102
views
Rooting a tree based on taxonomy of species
phylogeny
2 days ago by
lagartija
▴ 150
1
vote
0
replies
137
views
VQSR bias against rare variants
GATK
variant
VQSR
callling
2 days ago by
drabiza1
▴ 10
0
votes
1
reply
173
views
Problem using FastML for ancestral sequence reconstruction
FastML
message
reconstruction
fastml.std
ancestral
error
outdir
sequence
updated 2 days ago by
Mensur Dlakic
★ 19k • written 2 days ago by
CM
• 0
0
votes
0
replies
138
views
How do blastp step in MCScanX
MCScanX
2 days ago by
carlosgonzalezcruz327
▴ 10
3
votes
9
replies
4.1k
views
8 follow
aligner for CORRECTED pacbio long reads
pacbio
align
reads
sequencing
longreads
updated 2 days ago by
gconcepcion
▴ 280 • written 7.5 years ago by
cmo
▴ 90
25
votes
8
replies
23k
views
6 follow
What Is Ad (Allelic Depth) In 1000Genomes Vcf?
read
allele
genome
updated 2 days ago by
Maryam
• 0 • written 11.4 years ago by
Chronos
▴ 600
3
votes
3
replies
184
views
Extract sequence from Fasta using header
Fasta
updated 2 days ago by
GenoMax
117k • written 2 days ago by
Princy
▴ 40
0
votes
4
replies
767
views
analyzing a single cell and searching for a specific gene using single cell data
genomics
updated 1 day ago by
jared.andrews07
★ 13k • written 2 days ago by
Bioinfo
• 0
5
votes
2
replies
163
views
Extract header from fasta file
header
fasta
updated 2 days ago by
cpad0112
20k • written 2 days ago by
Princy
▴ 40
0
votes
0
replies
123
views
Job:
Data Engineer/Architect III to support CDC
public
health
bioinformatics
data
architect
informatics
big
2 days ago by
Alison Halpin
• 0
0
votes
2
replies
235
views
Best pipeline for RNAseq assembly and analysis (or help with stringtie assembly)
human
assembly
transcriptome
2 days ago by
Katherine
• 0
0
votes
1
reply
151
views
RNAseq (TruSeq stranded total RNA) - Stringtie fr-firststrand??
rnaseq
stranded
stringtie
updated 2 days ago by
grant.hovhannisyan
★ 2.4k • written 3 days ago by
Jirka
• 0
0
votes
3
replies
182
views
Incomplete alignment EMBOSS needleall
Alignment
updated 2 days ago by
lieven.sterck
14k • written 2 days ago by
bioinformatics.queries
▴ 50
2
votes
10
replies
314
views
bash script for merging R1 and R2 reads
illumina
fast.gz
bash
1 day ago by
ieie
▴ 10
1,000 results • Page
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Recent Votes
Gzip output of fasterq-dump
DESeq2 converting numeric to factor for unknown reason - SOLVED
DESeq2 converting numeric to factor for unknown reason - SOLVED
Tool similar to CollectGcBiasMetrics
pathway mapping of annotated genes (of bacteria)
C: what is in the fasta.fai
C: what is in the fasta.fai
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Recent Replies
Comment: doubts about SNAP, bioinformatic tools for gene prediction
by
lieven.sterck
14k
Hello https://www.biostars.org/u/110969/, Welcome to the forum! Please use the formatting bar (especially the `code` option) to present y…
Comment: How to find average read length and number of reads in a bam file using samtools
by
MobiusT
• 0
The size is 24661059 and I waited aroun 10 mins
Comment: Getting the best of RNA-Seq
by
ATpoint
62k
It is unclear to me what the question is. Do you want gene-level or transcript-level analysis? From what I know gene level analysis does no…
Answer: Computationally generated transcriptional regulation network
by
Matthias Zepper
▴ 910
Unfortunately, I have no experience whatsoever with yeast or GRN, but I recall [this article by de Boer et al.][1] that might be helpful. I…
Comment: Tool similar to CollectGcBiasMetrics
by
tea.vuki
▴ 10
it runs for a very long time, i wanted to know whether there's some shorter-running alternative
Comment: Tool similar to CollectGcBiasMetrics
by
Pierre Lindenbaum
146k
what's wrong with this tool ?
Comment: How to find average read length and number of reads in a bam file using samtools
by
Pierre Lindenbaum
146k
duplicate of your previous question : https://www.biostars.org/p/9528211/ > I used first samtools stats file.bam | grep "average length" b…
Answer: How to count the number of multimapped reads from a bam file?
by
Shred
▴ 640
Your question title doesn't fit properly the question body: please fix it. You're not counting multimapping reads based on your command s…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴ 100
Thanks and yes I had tried that but failed. I used the --const-fid (converts sample IDs to within-family IDs while setting all family IDs t…
Comment: Question regarding normalization in Seurat
by
ATpoint
62k
It is the sum of counts for that cell, so basically if a given cell has a given column in the count matrix it is the colSum of that column.
Answer: Clustered, annotated dotplot to scRNA-Seq data
by
fracarb8
▴ 810
Have a look at `Clustered_DotPlot` from `scCustomize`.
Comment: Align short sequence against ONT reads
by
kirillkirilenko.tomsk
• 0
It won't work because minimap2 aligns against a large reference sequence. What I want to do is to align each read in .fastq files against s…
Comment: PCA plot for miRNA
by
struggler
• 0
Hi Abhishek, For miRNA, first I predicted novel miRNA by miRDP2 and then aligning clean reads over it to get count file. 1>made database …
Answer: Align short sequence against ONT reads
by
colindaven
★ 3.8k
Very weird question, but .... - just use the gene/exon as a reference sequence - use minimap2 to align the ONT reads against this …
Comment: how to get a sequence from read fragments with ref sequence?
by
Aaron
• 0
Thank you. Let me try.
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