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245 results • Page
1 of 5
Sort: replies
Rank
Views
Votes
Replies
34
votes
30
replies
1.8k
views
6 follow
Tool:
BioFlows - Container-enabled Bioinformatics pipeline engine
workflow
next-gen
RNA-Seq
pipeline
updated 9 hours ago by
Ram
38k • written 2.3 years ago by
mfawzy.sami
▴ 90
16
votes
27
replies
5.4k
views
How can I easily remove overlapping transcripts, keeping only longest transcript, in a GFF file.
gff
parse
updated 3 hours ago by
Juke34
7.7k • written 4.5 years ago by
a.rex
▴ 350
8
votes
25
replies
1.9k
views
construction of a database
sql
noSQL
neo4j
database
updated 9 hours ago by
Ram
38k • written 22 months ago by
Debut
▴ 20
10
votes
21
replies
5.8k
views
12 follow
Easy way to split VCF file by chromosome
sequence
TOPMED
chromosome
Imputation
SNP
updated 21 minutes ago by
Joana
• 0 • written 14 months ago by
ConvolutedGenome
▴ 10
12
votes
20
replies
2.5k
views
Forum:
Starting a career in Bioinformatics
career
updated 9 hours ago by
Ram
38k • written 6.8 years ago by
rupashree.choudhury
▴ 10
27
votes
19
replies
3.8k
views
10 follow
Forum:
Google genomics cloud platform ?
genome
cloud
updated 3 hours ago by
Ram
38k • written 7.7 years ago by
GouthamAtla
12k
16
votes
19
replies
2.3k
views
7 follow
difficulty in underestanding terms and graphs
RNA-Seq
updated 9 hours ago by
Ram
38k • written 6.8 years ago by
DavidP
▴ 60
0
votes
16
replies
1.4k
views
How to convert ncbi gff file to ensembl gff format
bcftools
gff
updated 5 hours ago by
Ram
38k • written 6 months ago by
yoser4
▴ 10
11
votes
13
replies
4.1k
views
8 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 16 hours ago by
AtenaLia
▴ 20 • written 2.8 years ago by
Eugene A
▴ 170
4
votes
13
replies
909
views
6 follow
select rows in a tab-delimited ed file
linux
text
updated 5 hours ago by
Ram
38k • written 8 months ago by
S.O.T.AL-HASHIMI2
▴ 40
2
votes
12
replies
860
views
Generating vcf files per individual instead of one big file from bam files
vcf
bam
variant
updated 5 hours ago by
Ram
38k • written 7 months ago by
salman_96
▴ 70
4
votes
12
replies
1.1k
views
What is the command to download GTF from NCBI
ncbi
gtf
linux
updated 5 hours ago by
Ram
38k • written 8 months ago by
smithkthedale
▴ 10
3
votes
11
replies
441
views
prefix extraction and preparation for mapping and variant calling
bash
updated 9 hours ago by
GenoMax
127k • written 4 days ago by
Human
• 0
0
votes
11
replies
888
views
filtering multi sample vcf file
vcf
updated 5 hours ago by
Ram
38k • written 7 months ago by
Peerzada
• 0
10
votes
11
replies
3.2k
views
Forum:
48 Replicate RNA-Seq Study Points to Replicates Needed for DGE
RNA-seq
differential-gene-expression
updated 5 hours ago by
Ram
38k • written 7.9 years ago by
support
▴ 640
6
votes
11
replies
1.9k
views
Forum:
Archiving BAM files and analysis
archive
BAM
updated 3 hours ago by
Ram
38k • written 7.7 years ago by
seidel
11k
1
vote
11
replies
1.0k
views
Bacterial RNAseq - Help for beginner
next-gen
RNA-Seq
Bacteria
updated 9 hours ago by
Ram
38k • written 2.9 years ago by
liz.marjory
▴ 10
11
votes
11
replies
2.9k
views
8 follow
Forum:
Best open source genome browser in 2020
genome-browser
genomics
updated 9 hours ago by
Ram
38k • written 2.3 years ago by
mrmrwinter
▴ 30
6
votes
11
replies
677
views
Calculate RPKM
RPKM
19 hours ago by
Chris
▴ 70
6
votes
10
replies
2.5k
views
Genome assembly with RNA-seq data?
Assembly
genome
RNA-Seq
updated 9 hours ago by
Ram
38k • written 6.6 years ago by
Buffo
★ 2.0k
8
votes
10
replies
5.1k
views
gene filtering for agilent microarray using Limma
agilent microarray
limma
gene filtering
R
updated 11 hours ago by
Di Wu
• 0 • written 7.6 years ago by
rohit
▴ 60
1
vote
9
replies
2.6k
views
convert csv file to bed file
bed
updated 3 hours ago by
Ram
38k • written 13 months ago by
oldtownroald
• 0
8
votes
9
replies
2.3k
views
Forum:
Suggestions for small tools to add to Galaxy
Galaxy
updated 7 hours ago by
Ram
38k • written 7.9 years ago by
Devon Ryan
103k
4
votes
8
replies
1.1k
views
why those reads don't contain 0x2
bam
sam
updated 9 hours ago by
Ram
38k • written 17 months ago by
zt10122
▴ 20
11
votes
8
replies
598
views
How to perform synteny alignments and plots only with a gene?
Comparative
Evolution
Alignment
Synteny
Genomics
8 hours ago by
Rafael Soler
★ 1.1k
1
vote
8
replies
1.2k
views
Loading a pre-filtered loom file into pySCENIC
scRNA-seq
pySCENIC
loom
updated 5 hours ago by
Ram
38k • written 7 months ago by
Jacob
• 0
0
votes
8
replies
1.1k
views
How can i find longest sequence in fasta file on terminal
fasta
sequence
updated 8 hours ago by
Ram
38k • written 6 months ago by
logbio
▴ 30
3
votes
8
replies
1.9k
views
7 follow
Forum:
Bioinfomatic course or training for Computer Science professional
Training
Courses
updated 8 hours ago by
Ram
38k • written 5.5 years ago by
kianc
• 0
6
votes
8
replies
284
views
6 follow
Snakemake vs Nextflow Upcoming bioinformatics Project
Programming
Masters
3 hours ago by
rackbersingh
• 0
9
votes
7
replies
6.6k
views
6 follow
Multiple whole genome alignment
alignment
Assembly
sequencing
updated 4 hours ago by
Ram
38k • written 7.8 years ago by
robjohn7000
▴ 110
2
votes
7
replies
762
views
Import data for igraph using R
r
igraph
updated 4 hours ago by
Ram
38k • written 12 months ago by
kaisakaiho73847
• 0
0
votes
7
replies
1.1k
views
Convertion of FASTA file to FASTQ file
fasta
FASTQ
updated 5 hours ago by
Ram
38k • written 7 months ago by
sabreenaalam12345
• 0
4
votes
7
replies
2.4k
views
How can I deepen my knowledge in NGS data analysis?
ngs
gene
updated 8 hours ago by
Ram
38k • written 5.9 years ago by
AndyJian
• 0
6
votes
7
replies
419
views
Trying to install Roary with Conda results in error message
roary
conda
updated 8 hours ago by
ATpoint
70k • written 1 day ago by
tobiwan
▴ 10
9
votes
7
replies
888
views
How to work out coverage (100X) of WES using exome bed file?
bed
WES
coverage
updated 4 hours ago by
Ram
38k • written 11 months ago by
amy__
▴ 50
0
votes
7
replies
1.1k
views
Unable to convert from sam to bam file.
bam
sam
samtools
updated 3 hours ago by
Ram
38k • written 14 months ago by
usef
• 0
2
votes
6
replies
1.0k
views
GFF3 TO GTF CONVERSION
GFF3
Hydra
GFF
GTF
updated 3 hours ago by
Ram
38k • written 14 months ago by
Shagnik
• 0
3
votes
6
replies
1.7k
views
Methods and type datastructures use by Splign?
data-structure
splign
updated 9 hours ago by
Ram
38k • written 6.4 years ago by
Esaie
▴ 160
3
votes
6
replies
844
views
Change chromosome notation in bam file
bam
updated 4 hours ago by
Ram
38k • written 12 months ago by
Sara
• 0
3
votes
6
replies
742
views
How do we know that our contig sequence is really plasmid?
H.pylori
WGS
bacterial-genome
plasmid
updated 9 hours ago by
Ram
38k • written 13 months ago by
rickyalfaray
• 0
0
votes
6
replies
1.0k
views
how can I predict the interface site of RNA with protein
protein
prediction
RNA-Seq
updated 9 hours ago by
Ram
38k • written 3.8 years ago by
bangbang3332
• 0
2
votes
6
replies
613
views
Bad quality fastq files for analysis
quality
bad
DNA-seq
fastq
alignment
17 hours ago by
Gene_MMP8
▴ 220
10
votes
6
replies
2.5k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 4 hours ago by
Ram
38k • written 7.8 years ago by
lait
▴ 170
2
votes
5
replies
189
views
GATK GenotypeGVCFs explain
calling
gatk
variant
GenotypeGVCFs
updated 13 hours ago by
Pierre Lindenbaum
153k • written 15 hours ago by
Sarah
▴ 30
0
votes
5
replies
484
views
BAM file became smaller after merging
BAM
updated 4 hours ago by
Ram
38k • written 10 months ago by
kimmitzka
• 0
3
votes
5
replies
958
views
Change the interval of bed file
bed
updated 3 hours ago by
Ram
38k • written 14 months ago by
the
▴ 10
9
votes
5
replies
5.2k
views
Forum:
Can I switch back to wet lab in phd after doing a master in bioinformatics?
biology
wet-lab
phd
updated 7 hours ago by
Ram
38k • written 7.9 years ago by
blueearth205
▴ 10
5
votes
5
replies
4.8k
views
Which kind of microRNAs expression are measured in TCGA?
next-gen
RNA-Seq
genome
tcga
updated 9 hours ago by
Ram
38k • written 8.8 years ago by
jack
▴ 960
1
vote
5
replies
248
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
updated 6 hours ago by
Trivas
▴ 630 • written 13 hours ago by
TJay
• 0
2
votes
5
replies
495
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 4 hours ago by
igor
13k • written 4 days ago by
e.r.zakiev
▴ 30
245 results • Page
1 of 5
Recent Votes
A: Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
Comment: Plot in R: Presence of bacteria type A vs bacteria type B in different groups
Answer: Fastqc report analysis
Comment: Power analysis for patient samples
Comment: Snakemake vs Nextflow Upcoming bioinformatics Project
Comment: Snakemake vs Nextflow Upcoming bioinformatics Project
Answer: Creating a loop to mark duplicates using Picard
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Recent Replies
Comment: Easy way to split VCF file by chromosome
by
Joana
• 0
You need to run bcftools index on your vcf file before running the suggested command.
Comment: Fastqc report analysis
by
ntsopoul
▴ 20
I think you are fine, no worries. Will you go ahead an align the fastq files to a genome? Do you know how?
Comment: Fastqc report analysis
by
npavliukovec
• 0
Thanks for your answer, it really helped me. Also, I added --illumina options, because then I checked MultiQC report for all of my samples …
Answer: Fastqc report analysis
by
ntsopoul
▴ 20
Hi there, Cool that you learn to do these things and welcome to the bioinformatic community. In my opinion, both of the reports look to h…
Comment: Creating loop for read groups using Picard
by
Pierre Lindenbaum
153k
duplicate of https://www.biostars.org/p/9558127/
Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
by
Mensur Dlakic
★ 23k
Is there a problem in using program version that produced your top plot? Unless there is known bug in a program, or a super-useful feature…
Answer: Need help teasing out insertions and deletions with bcftools stats file.vcf > fi
by
Afif Elghraoui
• 0
Not in one step that I could find, but this works: deletions: ``` bcftools view --types indels --include 'ILEN<0' file.vcf | bcftools …
Comment: How to add gene information below the BSmooth result ?
by
diqixiaoyaoer
▴ 10
Thank you, sir. I have looked into your thesis. It's really great. I may have a try on Gviz if I don't have any idea about my question.
Comment: Snakemake vs Nextflow Upcoming bioinformatics Project
by
rackbersingh
• 0
Brilliant, thanks for the advice, i think after looking into what the community has said I have invested into learning the groovy language …
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
by
Juke34
7.7k
Change merge_loci to true
Comment: msigdbr returns the same genesets for mouse as in for human,
by
igor
13k
The addition of mouse-specific pathways to MSigDB is relatively recent. The package has not been updated to incorporate the latest version …
Comment: known-sites for Felis_catus_9.0 (GCA_000181335.4)
by
makarov
• 0
Thank you, I also found vcf files https://ftp.ensembl.org/pub/release-109/variation/vcf/felis_catus/
Comment: Creating a loop to mark duplicates using Picard
by
Ram
38k
For someone new at shell scripts, you're doing really well at using shell variables and parameter expansion. Good going!
Comment: Creating a loop to mark duplicates using Picard
by
brandnewatthis
• 0
Sorry, I am very new at this and am just learning my way around these symbols! Thanks for the help :)
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
by
BioinfoBee
• 0
its version 1.0.0. and installed using conda. How do I configure config.yaml file in such case?
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