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948 results • Page
1 of 19
Sort: replies
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Votes
Replies
8
votes
25
replies
1.9k
views
construction of a database
sql
noSQL
neo4j
database
updated 8 days ago by
Ram
38k • written 22 months ago by
Debut
▴ 20
9
votes
20
replies
3.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 7 days ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
9
votes
16
replies
2.9k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 7 days ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
0
votes
16
replies
1.4k
views
How to convert ncbi gff file to ensembl gff format
bcftools
gff
updated 8 days ago by
Ram
38k • written 7 months ago by
yoser4
▴ 10
7
votes
16
replies
2.0k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq
sequencing
updated 2 days ago by
Ram
38k • written 5.5 years ago by
Matteo Schiavinato
★ 3.6k
10
votes
15
replies
5.2k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 7 days ago by
Ram
38k • written 4.5 years ago by
marongiu.luigi
▴ 670
1
vote
15
replies
1.2k
views
Samtools merge Illumina and PB bam file empty
Illumina
samtools
Bam
PacBio
updated 7 days ago by
Ram
38k • written 2.6 years ago by
talbots
• 0
6
votes
13
replies
648
views
Error with STAR
STAR
updated 20 days ago by
Ram
38k • written 22 days ago by
Chris
▴ 70
2
votes
12
replies
551
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 5 days ago by
Ram
38k • written 7 days ago by
Human
• 0
6
votes
12
replies
1.2k
views
VCF files 101 - for people from non Bioinformatics Background
vcf
sequencing
genome
variant-calling
updated 16 days ago by
Ram
38k • written 2.6 years ago by
akshaykum684
▴ 20
0
votes
12
replies
1.5k
views
bedtools intersect issue
bed
bedtools
updated 7 days ago by
Ram
38k • written 4.6 years ago by
elisheva
▴ 120
6
votes
12
replies
1.1k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r
biomarker
updated 12 days ago by
Ram
38k • written 4.2 years ago by
english.server
▴ 290
8
votes
12
replies
2.5k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 12 days ago by
Ram
38k • written 19 months ago by
daver.v
▴ 30
6
votes
11
replies
762
views
Calculate RPKM
RPKM
8 days ago by
Chris
▴ 70
5
votes
11
replies
3.0k
views
Convert Plink to Arlequin
software-error
plink
Arlequin
PGDSpider
updated 15 days ago by
Ram
38k • written 4.9 years ago by
HG
▴ 30
2
votes
10
replies
1.2k
views
multiple FASTA sequnces in to one full sequnce according to their chromosome number
NGS
FASTA
bam
updated 12 days ago by
Ram
38k • written 4.1 years ago by
Anu
• 0
7
votes
10
replies
1.1k
views
col as names [solved]
R
updated 12 days ago by
Ram
38k • written 4.0 years ago by
demoraesdiogo2017
▴ 90
2
votes
10
replies
5.9k
views
fq.gz file use
BioEdit
R
updated 12 days ago by
Ram
38k • written 4.1 years ago by
choi.yisoo.hi
• 0
0
votes
10
replies
6.6k
views
Error: reads file does not look like a fastq file
fastq
bowtie2
ChIP-Seq
updated 12 days ago by
Ram
38k • written 6.5 years ago by
addilynn.beach
▴ 40
2
votes
9
replies
1.9k
views
SAM file quality check without converting into BAM
Alignment
SAM
updated 7 days ago by
Ram
38k • written 3.8 years ago by
vaish01kv
• 0
0
votes
9
replies
3.2k
views
Viral integration with RNA-seq data
ngs
RNA-seq
updated 6 days ago by
Ram
38k • written 5.5 years ago by
KVC_bioinfo
▴ 570
4
votes
9
replies
6.7k
views
bcftools consensus command
vcf
bcftools
updated 7 days ago by
Ram
38k • written 3.2 years ago by
Begonia_pavonina
▴ 90
0
votes
9
replies
2.9k
views
MATLAB Volcano Plot
Microarray
r
RNA-Seq
genome
updated 15 days ago by
Ram
38k • written 5.1 years ago by
bikash2510
▴ 30
1
vote
9
replies
2.6k
views
bam to fasta error using samtools
fasta
bam
updated 12 days ago by
Ram
38k • written 6.0 years ago by
christacaggiano
▴ 60
0
votes
9
replies
1.5k
views
Microarray analysis in R - target.txt,file,Sample info
R
updated 7 days ago by
Ram
38k • written 18 months ago by
bioinformatics
▴ 10
6
votes
9
replies
4.7k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 9 days ago by
Ram
38k • written 8.0 years ago by
gaurav.singh
▴ 10
2
votes
8
replies
9.1k
views
Size of typical genomic data
genomic
updated 2 days ago by
Ram
38k • written 4.9 years ago by
Nicolas Rosewick
10k
3
votes
8
replies
309
views
getting coding exon information from Ensembl API
Ensembl
API
updated 7 days ago by
Ram
38k • written 7 days ago by
Nobody
▴ 30
2
votes
8
replies
534
views
Depth of Coverage in Mitochondrial Genome with Samtools
samtools
depth-of-coverage
Mitochondrial-genome
10 days ago by
Lida
• 0
1
vote
8
replies
1.2k
views
Loading a pre-filtered loom file into pySCENIC
scRNA-seq
pySCENIC
loom
updated 8 days ago by
Ram
38k • written 7 months ago by
Jacob
• 0
1
vote
8
replies
398
views
Merge vcfs and retain only specific regions
SNPs
vcf
updated 21 days ago by
Ram
38k • written 22 days ago by
Clovering
▴ 30
0
votes
8
replies
5.1k
views
miRNA annotation from miRBase 21
miRBase
gene-annotation
next-gen
updated 20 days ago by
Ram
38k • written 8.5 years ago by
bioinforupesh2009.au
▴ 140
1
vote
8
replies
1.8k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 15 days ago by
Ram
38k • written 3.5 years ago by
mnazir
• 0
0
votes
7
replies
1.6k
views
File format for HGMD pro file flat
variant-analysis
HGMD
annovar
updated 7 days ago by
Ram
38k • written 4.2 years ago by
NB
▴ 960
6
votes
7
replies
1.1k
views
The size of the genome in pb of an organism before sequencing?
sequencing
genome
updated 2 days ago by
Ram
38k • written 4.4 years ago by
irg21
• 0
0
votes
7
replies
392
views
snpEff error when connecting to my built database
snpEff
22 days ago by
doggie
• 0
1
vote
7
replies
1.7k
views
Is anybody experiencing problems downloading from the SRA?
SRA
updated 6 days ago by
Ram
38k • written 2.4 years ago by
pomodoro_sinensis
▴ 90
1
vote
7
replies
512
views
Wildcard error in Snakemake - clarification on inputs
python
Snakemake
variant-calling
24 days ago by
DdogBoss
• 0
2
votes
7
replies
7.8k
views
linux 'cat' command merge fasta files without headers
fasta
linux
updated 23 days ago by
Ram
38k • written 8.8 years ago by
esterbuiate
• 0
1
vote
7
replies
1.7k
views
Platypus variantcaller.c:16971 errpr
platypus
updated 9 days ago by
Ram
38k • written 4.2 years ago by
nuketbilgen
▴ 40
1
vote
7
replies
1.2k
views
miRDeep2.pl cannot recognize reference fasta file
mirdeep2
fasta
mirna
mirdeep2.pl
mirna-sequencing
updated 12 days ago by
Ram
38k • written 3.1 years ago by
realnewbie
▴ 30
1
vote
7
replies
2.0k
views
Kallisto | bustools workflow for fastq with R1 and R2 (forward and reverse)?
scRNA-seq
Kallisto
bustools
updated 16 days ago by
Ram
38k • written 3.5 years ago by
Farah
▴ 80
1
vote
7
replies
2.1k
views
How to increase the speed of miRanda target prediction program?
miranada
mirna
parallel
updated 28 days ago by
kuttibiotech2009
▴ 30 • written 5.4 years ago by
lakhujanivijay
5.7k
6
votes
7
replies
4.4k
views
Creation Of A .Bed File From .Txt
plink
updated 2 days ago by
Ram
38k • written 9.2 years ago by
tom.d.brocklehurst
• 0
1
vote
7
replies
281
views
error bbduk
linux
bbduk
java
updated 14 days ago by
lieven.sterck
14k • written 14 days ago by
Kárita
• 0
1
vote
7
replies
1.1k
views
From a gene list to pathways
RNA-Seq
gene
updated 16 days ago by
Ram
38k • written 3.0 years ago by
eleonora.vercesi
• 0
1
vote
7
replies
951
views
Changing gene headers in .sqn file for genome upload NCBI
NCBI
sqn
UNIX
updated 12 days ago by
Ram
38k • written 2.8 years ago by
T_18
▴ 40
2
votes
7
replies
778
views
Import data for igraph using R
r
igraph
updated 8 days ago by
Ram
38k • written 12 months ago by
kaisakaiho73847
• 0
6
votes
7
replies
830
views
to mark the duplicates
Assembly
updated 16 days ago by
Ram
38k • written 3.8 years ago by
manubiomed20
▴ 10
0
votes
7
replies
1.1k
views
Unable to convert from sam to bam file.
bam
sam
samtools
updated 8 days ago by
Ram
38k • written 14 months ago by
usef
• 0
948 results • Page
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Recent Votes
Answer: Somatic truth set
Comment: Best way to visualize .paf or .sam alignment to a fasta file
Comment: Why not use ONLY promoter-bound peaks when testing for enrichment in differentia
Comment: Why not use ONLY promoter-bound peaks when testing for enrichment in differentia
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Answer: Variant caller reports a homozygous variant genotype, but more reads are associa
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Comment: Kallisto bustools for scRNA-seq
by
dsull
★ 4.0k
I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
Comment: Aberrant splicing in bulk RNAseq
by
dsull
★ 4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell
by
lethalfang
▴ 90
There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6. There is also a CNA preprint from years ago b…
Comment: Somatic truth set
by
lethalfang
▴ 90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata?
by
jv
★ 1.0k
Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"? An alternative option is the following: ``` idx <- whi…
Comment: GO enrichment analysis
by
Jeremy
▴ 770
g:Profiler has an Arabidopsis option: [g:Profiler][1] [1]: https://biit.cs.ut.ee/gprofiler/gost
Answer: Any tips in landing a bioinformatic job?
by
Carambakaracho
★ 3.2k
The first job is a nightmare and you will need some luck. I understand you're looking for an industry offering. Unfortunately I've worked o…
Comment: Best way to visualize .paf or .sam alignment to a fasta file
by
GenoMax
127k
Why not use IGV with SAM file? If you want a text based viewer then ASCIIGenome: https://asciigenome.readthedocs.io/en/latest/
Answer: What is the NCBI's definition of an "atypical genome"?
by
MirianT_NCBI
▴ 490
Hi, You can find more information about what constitute an [atypical genome in this FAQ][1]. Here's the list of reasons for a genome to …
Comment: How to get subset of a Seurat object based on metadata?
by
sunyeping
▴ 80
> skin$predicted_cell_type Error in rep.int(x = colnames(x = x), times = length(x = i)) : unimplemented type 'NULL' in 'rep3…
Comment: using CITE-seq data to cluster single cells
by
chi.delta
▴ 40
Let's say that based on known FACS data, I already know that three populations exist based on the two antibodies staining: single positive …
Answer: syntax errors when running part3 all-against-all
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Adrian Altenhoff
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Dear Sofia, this looks like the all-vs-all file is corrupted. maybe a race condition of to processes that tried to write the same file. …
Answer: Any tips in landing a bioinformatic job?
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zhousun21
▴ 40
Since you are just starting out, I suggest sending your resume to a few recruiters who specialize in science placements. They will intervie…
Comment: How to get subset of a Seurat object based on metadata?
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Do you have cells labeled "0:CD8 T Cell" in `skin$predicted_cell_type`?
Comment: using CITE-seq data to cluster single cells
by
ATpoint
70k
Think about it, how would any clustering with only two genes/features be informative? Is this really what you need? If you break it down, f…
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