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102,848 results • Page
1 of 2057
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
15
views
Error with TCGA package - TCGAbiolinks
TCGA
r
cancer
2 hours ago by
JACKY
▴ 10
0
votes
0
replies
14
views
Question about rMATS output files
rMATS
novel
2 hours ago by
Lillian
• 0
678
votes
160
replies
88k
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
1
vote
6
replies
246
views
ESTIMATE tumor purity
purity
r
cancer
2 hours ago by
JACKY
▴ 10
0
votes
4
replies
113
views
Exctract unmapped reads from BLAST
blatella
unmapped
germanica
annotation
blast
trinotate
updated 3 hours ago by
GenoMax
117k • written 7 hours ago by
Pilar
• 0
4
votes
3
replies
4.5k
views
Resfams Database usage
Resfams
updated 4 hours ago by
Neel
▴ 10 • written 6.1 years ago by
ginna
▴ 10
0
votes
0
replies
50
views
Searching for RNA-seq melanoma samples in TCGA or cBioPortal
TCGA
r
cBioPortal
cancer
8 hours ago by
JACKY
▴ 10
0
votes
1
reply
259
views
Quast Ouput
Contig
Quast
updated 13 hours ago by
Ying
• 0 • written 9 months ago by
kishorssf91
• 0
0
votes
1
reply
110
views
SRA obtained metagenomic reads appears to corrupt - cannot work on SingleM
SingleM
SRAtoolkit
updated 3 hours ago by
GenoMax
117k • written 16 hours ago by
rfour92
• 0
0
votes
1
reply
177
views
Get nucleotide sequence of assembled RNA transcripts
transcript
assembly
RNA-seq
chimeric
RNA
updated 23 hours ago by
tomas4482
▴ 140 • written 12 days ago by
drabiza1
▴ 10
1
vote
0
replies
102
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
130
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
98
views
Estimating gene family size changes for a large tree?
Phylogenetics
CAFE5
20 hours ago by
Rijan
▴ 30
1
vote
2
replies
180
views
Quick way to get a field such as QNAME from the last read in a bam file?
bam
samtools
17 hours ago by
kalavattam
▴ 70
1
vote
1
reply
161
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 1 day ago by
kalavattam
▴ 70
0
votes
1
reply
99
views
converting a DocumentTermMatrix to factor
DocumentTermMatrix
convert
factor
offtopic
updated 1 day ago by
cpad0112
20k • written 1 day ago by
hasani.iut6
▴ 70
0
votes
0
replies
80
views
Rooting a tree based on taxonomy of species
phylogeny
1 day ago by
lagartija
▴ 150
1
vote
0
replies
114
views
VQSR bias against rare variants
GATK
variant
VQSR
callling
1 day ago by
drabiza1
▴ 10
0
votes
1
reply
148
views
Problem using FastML for ancestral sequence reconstruction
FastML
message
reconstruction
fastml.std
ancestral
error
outdir
sequence
updated 1 day ago by
Mensur Dlakic
★ 19k • written 1 day ago by
CM
• 0
0
votes
0
replies
117
views
How do blastp step in MCScanX
MCScanX
1 day ago by
carlosgonzalezcruz327
▴ 10
3
votes
9
replies
4.0k
views
8 follow
aligner for CORRECTED pacbio long reads
pacbio
align
reads
sequencing
longreads
updated 1 day 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 1 day ago by
Maryam
• 0 • written 11.4 years ago by
Chronos
▴ 600
3
votes
3
replies
154
views
Extract sequence from Fasta using header
Fasta
updated 1 day ago by
GenoMax
117k • written 1 day ago by
Princy
▴ 40
0
votes
0
replies
99
views
How to count the number of multimapped reads from a bam file?
rnaseq
mapping
bowtie2
featurecounts
1 day ago by
O.rka
▴ 600
0
votes
4
replies
701
views
analyzing a single cell and searching for a specific gene using single cell data
genomics
updated 19 hours ago by
jared.andrews07
★ 13k • written 1 day ago by
Bioinfo
• 0
5
votes
2
replies
140
views
Extract header from fasta file
header
fasta
updated 1 day ago by
cpad0112
20k • written 1 day ago by
Princy
▴ 40
0
votes
0
replies
101
views
Job:
Data Engineer/Architect III to support CDC
public
health
bioinformatics
data
architect
informatics
big
1 day ago by
Alison Halpin
• 0
0
votes
2
replies
205
views
Best pipeline for RNAseq assembly and analysis (or help with stringtie assembly)
human
assembly
transcriptome
1 day ago by
Katherine
• 0
0
votes
1
reply
128
views
RNAseq (TruSeq stranded total RNA) - Stringtie fr-firststrand??
rnaseq
stranded
stringtie
updated 2 days ago by
grant.hovhannisyan
★ 2.4k • written 2 days ago by
Jirka
• 0
0
votes
3
replies
156
views
Incomplete alignment EMBOSS needleall
Alignment
updated 1 day ago by
lieven.sterck
14k • written 2 days ago by
bioinformatics.queries
▴ 50
2
votes
10
replies
285
views
bash script for merging R1 and R2 reads
illumina
fast.gz
bash
1 day ago by
ieie
▴ 10
0
votes
3
replies
143
views
Retrieve nucleotide ID from protein ID
refseq
entrez
bipython
updated 2 days ago by
vkkodali_ncbi
★ 3.3k • written 2 days ago by
kmears
• 0
0
votes
0
replies
94
views
TCGA data downloaded from GDC
TCGA
2 days ago by
Mamta
▴ 500
2
votes
2
replies
238
views
pymol for superimpose by python script
png
python
superimposition
pymol
print
1 day ago by
iamsmor
• 0
0
votes
3
replies
161
views
Scaling for p.heatmap
variance
p.heatmap
scaling
unit
1 day ago by
bnayer26
• 0
4
votes
4
replies
194
views
what is better to use in single cell
genomics
offtopic
updated 2 days ago by
Friederike
8.4k • written 2 days ago by
Bioinfo
• 0
0
votes
4
replies
213
views
Difference in number of DEGs from Deseq2 and limma-voom
RNAseq
Deseq2
limma
2 days ago by
dzisis1986
▴ 40
0
votes
2
replies
143
views
Gene expression assay Yeast sample prep
in
cells
Live
study
2 days ago by
dshdixit
▴ 10
1
vote
1
reply
173
views
ggscatter, gene expression, correlation
RNA-Seq
plot
scatter
updated 2 days ago by
Trivas
▴ 370 • written 2 days ago by
Rob
▴ 120
1
vote
0
replies
94
views
Interpretation of '1|2' in GT field and '0|1' in PGT field
GVCF
calling
GATK
SNP
VCF
2 days ago by
Choi
▴ 10
1
vote
1
reply
430
views
Software/packages for analyzing differential isoforms from RNA-seq data?
RNA-Seq
rna-seq
sequencing
next-gen
updated 2 days ago by
Antonio R. Franco
★ 4.8k • written 19 months ago by
Kai_Qi
▴ 120
1
vote
2
replies
315
views
Samtools Failing to Install through Conda
samtools
conda
updated 2 days ago by
jambler24
• 0 • written 8 weeks ago by
jjp55
▴ 20
1
vote
2
replies
157
views
BLAST IN CLC vs BLAST IN NCBI website
BLAST
computational
biology
2 days ago by
lukhanyomakhabane
▴ 20
0
votes
0
replies
98
views
Cell Type and Gene Specific Survival Analysis in scRNA-seq
TCGA
scRNA-seq
2 days ago by
Ergün
▴ 20
0
votes
3
replies
173
views
how to get a sequence from read fragments with ref sequence?
reads
fragments
reference
assembly
sequence
updated 2 days ago by
Pierre Lindenbaum
146k • written 2 days ago by
Aaron
• 0
0
votes
1
reply
128
views
metagenome binning using MaxBin2 for each dataset
Metagenome
Binning
MaxBin
updated 2 days ago by
andres.firrincieli
★ 2.5k • written 2 days ago by
serene.s
• 0
1
vote
4
replies
245
views
bcftools index error: [E::bgzf_read_block] Invalid BGZF header at offset 12889964510
bcftools
updated 2 days ago by
cmdcolin
★ 2.2k • written 2 days ago by
biostars
▴ 10
0
votes
1
reply
154
views
Get cleaved SARS-CoV-2 protein sequences (all major variants)?
motif
variant
Python
SARS-CoV-2
cleavage
updated 2 days ago by
GenoMax
117k • written 2 days ago by
ngarber
• 0
0
votes
0
replies
141
views
How do I run pal2nal.pl in batch mode ?
gene
genome
protein
2 days ago by
Ramana
• 0
2
votes
2
replies
186
views
Plink runtime when using "--extract"
plink2
bgen
2 days ago by
Stochasticity
• 0
102,848 results • Page
1 of 2057
Recent Votes
Answer: ESTIMATE tumor purity
C: Run PHI-BLAST in BLAST+ standalone
Answer: Junior bioinformatician in italy
Junior bioinformatician in italy
A: Thoughts on switching from Biology to Bioinformatics
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
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Recent Awards •
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▴ 10
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Marco Pannone
▴ 290
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Recent Replies
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
chrchang523
9.3k
If 1kgtot.bim contains doubled IDs (e.g. "HG00096 HG00096", you need to provide a doubled ID to `--indv`. The log file shows that your scr…
Answer: ESTIMATE tumor purity
by
JACKY
▴ 10
Just in case anyone faces this problem in the future, here is the link for the updated `estimate package` on github: https://github.com/…
Answer: Exctract unmapped reads from BLAST
by
GenoMax
117k
> Is there a way to tell blast to output the unmapped reads into a > separate file? No there is not. You will need to use `-outfmt 7` whe…
Comment: Resfams Database usage
by
Neel
▴ 10
Hi, i have annotated genome by prokka and o want to search amr agaisnt resfams could you please tell me how to do it steps by steps.
Comment: Exctract unmapped reads from BLAST
by
Pierre Lindenbaum
146k
those are two distinct commands https://linux.die.net/man/1/comm and https://linux.die.net/man/1/join extract the names of your queries, s…
Comment: Exctract unmapped reads from BLAST
by
Pilar
• 0
Thanks for answering :), sorry, I'm new at this. These are commands I should use when I launch Blast in terminal?
Comment: Exctract unmapped reads from BLAST
by
Pierre Lindenbaum
146k
have a look at `comm` or `join`.
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴ 100
Sorry I forgot to mention I used it in this loop, which worked with another plink file, but not with this 1KG file. for popfile in $(l…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
chrchang523
9.3k
`--indv` takes a single ID, not a filename. So `--indv IDlist.txt` shouldn't work.
Answer: Quast Ouput
by
Ying
• 0
The "# contigs 47484" is based on contig of size >= 500 bp (see the first line of your screenshot). The "# contigs (>= 0 bp)" is the raw nu…
Answer: SRA obtained metagenomic reads appears to corrupt - cannot work on SingleM
by
Mensur Dlakic
★ 19k
Not sure why: 1) you are splitting reads; 2) you are fixing reads when they seem fine. I suggest something like this instead after `prefetc…
Comment: Quick way to get a field such as QNAME from the last read in a bam file?
by
kalavattam
▴ 70
Thank you. Do you know of any strategies for non-coordinated-sorted bam files?
Comment: analyzing a single cell and searching for a specific gene using single cell data
by
jared.andrews07
★ 13k
@rpolicastro gave you several helpful links for using the h5ad file, in addition to how to explore and plot data. The links in my answer al…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴ 100
I was able to run the --indv command successfully on a file with a bed file by simply listing the IDs in single column. However, with anoth…
Answer: Get nucleotide sequence of assembled RNA transcripts
by
tomas4482
▴ 140
1. design a RNA-seq experiment specifically seuqencing non-coding RNA/circRNA sequencing. 2. subset to interested region -> extract chi…
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