Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
508 results • Page
1 of 11
Sort: replies
Rank
Views
Votes
Replies
8
votes
25
replies
1.9k
views
construction of a database
sql
noSQL
neo4j
database
updated 2 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 1 day 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 1 day 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 2 days ago by
Ram
38k • written 7 months ago by
yoser4
▴ 10
1
vote
15
replies
1.2k
views
Samtools merge Illumina and PB bam file empty
Illumina
samtools
Bam
PacBio
updated 1 day ago by
Ram
38k • written 2.6 years ago by
talbots
• 0
10
votes
15
replies
5.2k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 1 day ago by
Ram
38k • written 4.5 years ago by
marongiu.luigi
▴ 670
8
votes
12
replies
2.4k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 6 days ago by
Ram
38k • written 19 months ago by
daver.v
▴ 30
6
votes
12
replies
1.1k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r
biomarker
updated 6 days ago by
Ram
38k • written 4.2 years ago by
english.server
▴ 290
0
votes
12
replies
1.5k
views
bedtools intersect issue
bed
bedtools
updated 1 day ago by
Ram
38k • written 4.6 years ago by
elisheva
▴ 120
6
votes
11
replies
712
views
Calculate RPKM
RPKM
3 days ago by
Chris
▴ 70
1
vote
11
replies
433
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 2 hours ago by
GenoMax
127k • written 1 day ago by
Human
• 0
2
votes
10
replies
1.2k
views
multiple FASTA sequnces in to one full sequnce according to their chromosome number
NGS
FASTA
bam
updated 6 days ago by
Ram
38k • written 4.1 years ago by
Anu
• 0
2
votes
10
replies
5.9k
views
fq.gz file use
BioEdit
R
updated 6 days ago by
Ram
38k • written 4.1 years ago by
choi.yisoo.hi
• 0
7
votes
10
replies
1.1k
views
col as names [solved]
R
updated 6 days ago by
Ram
38k • written 4.0 years ago by
demoraesdiogo2017
▴ 90
0
votes
10
replies
6.6k
views
Error: reads file does not look like a fastq file
fastq
bowtie2
ChIP-Seq
updated 6 days ago by
Ram
38k • written 6.5 years ago by
addilynn.beach
▴ 40
4
votes
9
replies
6.7k
views
bcftools consensus command
vcf
bcftools
updated 1 day ago by
Ram
38k • written 3.2 years ago by
Begonia_pavonina
▴ 90
1
vote
9
replies
2.6k
views
bam to fasta error using samtools
fasta
bam
updated 6 days ago by
Ram
38k • written 6.0 years ago by
christacaggiano
▴ 60
0
votes
9
replies
3.2k
views
Viral integration with RNA-seq data
ngs
RNA-seq
updated 18 hours ago by
Ram
38k • written 5.5 years ago by
KVC_bioinfo
▴ 570
0
votes
9
replies
1.5k
views
Microarray analysis in R - target.txt,file,Sample info
R
updated 1 day ago by
Ram
38k • written 18 months ago by
bioinformatics
▴ 10
2
votes
9
replies
1.9k
views
SAM file quality check without converting into BAM
Alignment
SAM
updated 1 day ago by
Ram
38k • written 3.8 years ago by
vaish01kv
• 0
6
votes
9
replies
4.7k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 3 days ago by
Ram
38k • written 7.9 years ago by
gaurav.singh
▴ 10
3
votes
8
replies
275
views
getting coding exon information from Ensembl API
Ensembl
API
updated 1 day ago by
Ram
38k • written 2 days ago by
Nobody
▴ 30
3
votes
8
replies
379
views
How to find promoter sequence of a gene?
promoter
19 hours ago by
sunyeping
▴ 40
1
vote
8
replies
1.2k
views
Loading a pre-filtered loom file into pySCENIC
scRNA-seq
pySCENIC
loom
updated 2 days ago by
Ram
38k • written 7 months ago by
Jacob
• 0
2
votes
8
replies
494
views
Depth of Coverage in Mitochondrial Genome with Samtools
samtools
depth-of-coverage
Mitochondrial-genome
5 days ago by
Lida
• 0
1
vote
7
replies
856
views
Splitting BED file by technical replicate or extract all unique barcodes
BED
updated 1 day ago by
Ram
38k • written 2.6 years ago by
summer_researcher
• 0
0
votes
7
replies
1.1k
views
Unable to convert from sam to bam file.
bam
sam
samtools
updated 2 days ago by
Ram
38k • written 14 months ago by
usef
• 0
1
vote
7
replies
1.7k
views
Platypus variantcaller.c:16971 errpr
platypus
updated 3 days ago by
Ram
38k • written 4.2 years ago by
nuketbilgen
▴ 40
1
vote
7
replies
946
views
Changing gene headers in .sqn file for genome upload NCBI
NCBI
sqn
UNIX
updated 6 days ago by
Ram
38k • written 2.8 years ago by
T_18
▴ 40
2
votes
7
replies
773
views
Import data for igraph using R
r
igraph
updated 2 days ago by
Ram
38k • written 12 months ago by
kaisakaiho73847
• 0
4
votes
7
replies
2.0k
views
How to move the files from sub folder and sub-sub folders into one other folder?
bash
updated 1 day ago by
Ram
38k • written 21 months ago by
mathavanbioinfo
▴ 70
1
vote
7
replies
1.1k
views
Bulk download tomato RNA or cDNA sequences (partial) with genomic loci list
SGN
tomato
updated 22 hours ago by
Ram
38k • written 5.0 years ago by
donger1103
▴ 10
1
vote
7
replies
1.2k
views
miRDeep2.pl cannot recognize reference fasta file
mirdeep2
fasta
mirna
mirdeep2.pl
mirna-sequencing
updated 6 days ago by
Ram
38k • written 3.0 years ago by
realnewbie
▴ 30
0
votes
7
replies
1.6k
views
File format for HGMD pro file flat
variant-analysis
HGMD
annovar
updated 1 day ago by
Ram
38k • written 4.2 years ago by
NB
▴ 960
1
vote
7
replies
1.7k
views
Is anybody experiencing problems downloading from the SRA?
SRA
updated 22 hours ago by
Ram
38k • written 2.3 years ago by
pomodoro_sinensis
▴ 90
2
votes
6
replies
1.0k
views
GFF3 TO GTF CONVERSION
GFF3
Hydra
GFF
GTF
updated 2 days ago by
Ram
38k • written 14 months ago by
Shagnik
• 0
0
votes
6
replies
1.1k
views
Raw data for chromosome 21
WCS
bam
sequencing
updated 1 day ago by
Ram
38k • written 4.0 years ago by
tamara912
• 0
0
votes
6
replies
481
views
Issue in import files in Metaboanalyst
Metaboanalyst
R
updated 6 days ago by
Ram
38k • written 6 weeks ago by
Andrea
▴ 10
1
vote
6
replies
1.0k
views
gff file
GFF
UNIPRTOT
updated 1 day ago by
Ram
38k • written 18 months ago by
devhimd
▴ 10
0
votes
6
replies
444
views
Recreating a SPAdes Assembly
fasta
SPAdes
Assembly
BAM
updated 6 days ago by
Ram
38k • written 4 weeks ago by
Rene
• 0
1
vote
6
replies
946
views
problem for comparing 2 type of annotation file
gencode
RNA-Seq
TCGA
updated 22 hours ago by
Zhenyu Zhang
▴ 750 • written 4.8 years ago by
modarzi
▴ 160
2
votes
6
replies
253
views
bioinformatics problems solved by graphs data structure
Graph
algorithm
data-structure
updated 16 hours ago by
Ram
38k • written 22 hours ago by
abdelmalek.benmeziane
• 0
7
votes
6
replies
1.3k
views
How to get/calculate coverage of a gene using bed file?
bed
coverage
gene
updated 1 day ago by
Ram
38k • written 16 months ago by
Nikhil
▴ 10
5
votes
6
replies
2.9k
views
Changes log2FC values of DESeq2
log2FC
DESeq2
updated 22 hours ago by
Ram
38k • written 5.2 years ago by
realnewbie
▴ 30
3
votes
6
replies
1.7k
views
Methods and type datastructures use by Splign?
data-structure
splign
updated 2 days ago by
Ram
38k • written 6.4 years ago by
Esaie
▴ 160
10
votes
6
replies
2.6k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 2 days ago by
Ram
38k • written 7.8 years ago by
lait
▴ 170
0
votes
5
replies
2.5k
views
Recoding plink file from 12 to 01
plink
plink2chromopaiter.pl
updated 22 hours ago by
Ram
38k • written 5.2 years ago by
dirranrak
▴ 20
0
votes
5
replies
489
views
BAM file became smaller after merging
BAM
updated 2 days ago by
Ram
38k • written 11 months ago by
kimmitzka
• 0
0
votes
5
replies
779
views
Inquiry related to vcf file and formatting
vcf
bcftools
updated 1 day ago by
Ram
38k • written 19 months ago by
rheab1230
▴ 140
1
vote
5
replies
308
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
updated 2 days ago by
Trivas
▴ 700 • written 3 days ago by
TJay
• 0
508 results • Page
1 of 11
Recent Votes
vg paired end short read mapping: Best practice?
Raxml continue interrupted bootstrap run
Comment: How to find promoter sequence of a gene?
Comment: in an RNA-seq experiment, what threshold would you use to define a set of expres
A: Multiple Blast Output Formats From 1 Blast Run
Multiple Blast Output Formats From 1 Blast Run
Answer: query UCSC db for CDS coordinates (Gencode)
Recent Locations •
All
France/Nantes/Institut du Thorax - INSERM UMR1087,
just now
Hungary,
1 minute ago
France,
2 minutes ago
United Kingdom,
2 minutes ago
Tübingen,
3 minutes ago
Belgium, Brussels,
5 minutes ago
Canada,
5 minutes ago
Recent Awards •
All
Popular Question
to
farzaneafzali
▴ 70
Scholar
to
MirianT_NCBI
▴ 460
Popular Question
to
Ap1438
▴ 50
Popular Question
to
genomes_and_MGEs
▴ 10
Popular Question
to
txema.heredia
▴ 70
Popular Question
to
anu014
▴ 190
Popular Question
to
Dude
• 0
Recent Replies
Comment: How to colour points in cnetplot of clustprofiler?
by
mrmodenait
• 0
Hey guys! I think I may have an answer to your question. So to change the colour of the gene points, you need to supply a vector to `foldCh…
Comment: Active enhancers for mm39
by
Matthias Zepper
3.4k
Then using the enhancers called using [by the FANTOM5][1] project is likely the most promising approach. Since they [are defined by CAGE-se…
Comment: Problem with fatsq-dump
by
GenoMax
127k
> But the command fastq-dump SRR1972917 does not. What does it not do? What do you get when you try `which fastq-dump`? I just checked tha…
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
by
ATpoint
70k
Please google what the Benjamini-Hochberg correction is and what it does. In a nutshell, it corrects for multiple testing, outputting these…
Comment: query UCSC db for CDS coordinates (Gencode)
by
GenoMax
127k
> it's hard to discover what's new, what already exists, what's the > purpose of each tool . samtools, gatk etc... have a release page on >…
Comment: query UCSC db for CDS coordinates (Gencode)
by
Pierre Lindenbaum
153k
1) it's fun :-D 2) there's is a bunch of amazing tools under https://hgdownload.soe.ucsc.edu/admin/exe/ but it's hard to discover what's …
Comment: how to get to a VCF from bam files
by
GenoMax
127k
If you only have BAM files you need in the directory you are working in then `*.bam` would be ok. Most people working with human samples ca…
Answer: query UCSC db for CDS coordinates (Gencode)
by
Maximilian Haeussler
★ 1.5k
The UCSC command line tool for this operation is "genePredToBed". To break a BED into one line per exon, use "bedToExons". The tools can be…
Comment: in an RNA-seq experiment, what threshold would you use to define a set of expres
by
i.sudbery
16k
Try: https://bioinformatics.stackexchange.com/questions/687/what-methods-are-available-to-find-a-cutoff-value-for-non-expressed-genes-in-rn…
Answer: GetBM - GERP conservation score for GRCm39
by
Ben_Ensembl
★ 2.2k
Hi Kyle, The GERP scores are not available through BioMart (nor the Ensembl REST API). The most efficient method for retrieving these scor…
Comment: how to get to a VCF from bam files
by
Human
• 0
Ok, but in general this approach would work? And why would I not want to use all the bam and Bam.bai files? Why would I subset it?
Comment: in an RNA-seq experiment, what threshold would you use to define a set of expres
by
ATpoint
70k
This has been asked many times before. Please google for 'fpkm cutoff biostars', 'expressed cutoff biostars' or similar queries. With some …
Answer: GetBM - GERP conservation score for GRCm39
by
Mike Smith
★ 2.0k
You can try using `searchAttributes()` which at least means you don't have to look at every possible attribute hoping to find the one you n…
Answer: Calculation method of RMSMappingQuality
by
zhoujun.nmu
• 0
Hello, Have you solved this probelm?
Comment: PCA in gene expression
by
ali
• 0
Thanks for your help Dear i.sudbery I have been working on a project related to the correlation between genetic mutations and drug resis…
Traffic: 2499 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6