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14,233 results • Page
2 of 285
Sort: Views
Rank
Views
Votes
Replies
34
votes
11
replies
44k
views
8 follow
Where Can I Download Some Bam Files?
bam
RNA-seq
updated 3 months ago by
Ram
43k • written 11.9 years ago by
snakesgun
▴ 160
25
votes
9
replies
44k
views
Converting Gff To Bed With Bedtools?
gff
bed
bedtools
updated 7 weeks ago by
Ram
43k • written 11.2 years ago by
user
▴ 940
35
votes
14
replies
43k
views
9 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf
bcftools
updated 5 months ago by
ashotmarg2004
▴ 130 • written 7.7 years ago by
William
★ 5.2k
121
votes
35
replies
43k
views
20 follow
Forum:
Snakemake vs. Nextflow: strengths and weaknesses
snakemake
nextflow
updated 10 months ago by
Ram
43k • written 6.8 years ago by
ropolocan
▴ 810
46
votes
9
replies
43k
views
7 follow
Tool:
Tools to merge overlapping paired-end reads
ngs
Assembly
fastq
updated 11 months ago by
Charles-Alexandre Roy
▴ 40 • written 7.3 years ago by
Abdul Rafay Khan
★ 1.2k
47
votes
9
replies
43k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 8 weeks ago by
Picasa
▴ 640 • written 7.4 years ago by
ZheFrench
▴ 550
105
votes
26
replies
42k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 6 months ago by
zx8754
11k • written 11.2 years ago by
henryvuong
▴ 810
81
votes
21
replies
42k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed
transcript
ucsc
biomart
updated 6 months ago by
Joel Wallenius
▴ 210 • written 10.1 years ago by
pristanna
▴ 750
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing
fastq
updated 4 months ago by
Pierre Lindenbaum
160k • written 14.0 years ago by
Zach Stednick
▴ 660
120
votes
33
replies
39k
views
24 follow
Forum:
Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 10 months ago by
carlopecoraro2
★ 2.4k • written 10.6 years ago by
Eric Normandeau
11k
19
votes
10
replies
38k
views
Ensembl ID to Gene Symbol
gene-symbol
updated 9 months ago by
Ram
43k • written 7.9 years ago by
Pranavathiyani G
▴ 330
6
votes
25
replies
38k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 10 months ago by
13554221497
• 0 • written 6.0 years ago by
ARich
▴ 130
23
votes
4
replies
37k
views
bcftools compressing and indexing vcf files
sequence
bcftools
vcf
index
updated 4 months ago by
GenoMax
140k • written 5.6 years ago by
Inquisitive8995
▴ 270
27
votes
21
replies
37k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 5 months ago by
Axzd
▴ 50 • written 9.7 years ago by
onter
▴ 170
13
votes
6
replies
37k
views
generating genome indexes with STAR
RNA-Seq
STAR
updated 8 months ago by
DareDevil
★ 4.3k • written 7.8 years ago by
snp87
▴ 60
10
votes
5
replies
37k
views
How to compare 2 VCF files
vcf
SNP
updated 9 months ago by
Ram
43k • written 9.9 years ago by
Parimala Devi
▴ 100
80
votes
21
replies
36k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 4 months ago by
kathryn.jacksonjones
• 0 • written 9.9 years ago by
M K
▴ 650
50
votes
18
replies
36k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq
macs
ChIP-Seq
peaks
updated 9 months ago by
Ram
43k • written 7.6 years ago by
igor
13k
21
votes
8
replies
36k
views
8 follow
Merging/Concatenating Vcf Files
vcftools
snp
indel
updated 7 months ago by
Bioinformatics_NewComer
▴ 330 • written 11.6 years ago by
bioinfo
▴ 830
74
votes
15
replies
36k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing
duplicates
updated 4 months ago by
Ram
43k • written 13.9 years ago by
Pierre Lindenbaum
160k
39
votes
16
replies
36k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 3 months ago by
GenoMax
140k • written 3.6 years ago by
lavinia.gordon
▴ 160
31
votes
10
replies
35k
views
8 follow
Convert between RefSeq and Ensembl Transcript?
refseq
ensembl
updated 8 months ago by
Ram
43k • written 9.7 years ago by
pwg46
▴ 520
197
votes
27
replies
34k
views
20 follow
Forum:
Bioinformatics Cartoon
bioinformatics
updated 8 months ago by
Ram
43k • written 12.2 years ago by
Maxime Lamontagne
★ 2.3k
13
votes
12
replies
34k
views
Estimating Insert Size From Paired End Data.
picard
alignment
paired-end
updated 6 months ago by
Ram
43k • written 10.1 years ago by
GouthamAtla
12k
19
votes
10
replies
34k
views
6 follow
read depth using samtools
depth
samtools
updated 6 months ago by
Sachin
• 0 • written 5.2 years ago by
LimMo
▴ 30
28
votes
11
replies
34k
views
10 follow
Samtools View: Only Forward Or Reverse Strand
samtools
strand
updated 9 weeks ago by
shaoqian ma
• 0 • written 12.4 years ago by
Gregor Rot
▴ 540
39
votes
23
replies
33k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 6 months ago by
s.w.vanderlaan
▴ 40 • written 2.7 years ago by
Michal Nevo
▴ 130
42
votes
16
replies
33k
views
14 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 6 months ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
chparada
▴ 70
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 4 months ago by
Ram
43k • written 10.4 years ago by
Irsan
★ 7.8k
67
votes
15
replies
33k
views
14 follow
Rna-Seq Pipeline
pipeline
next-gen-sequencing
rna
rna-seq
updated 10 months ago by
Ram
43k • written 13.9 years ago by
brentp
24k
36
votes
11
replies
32k
views
6 follow
Sjdboverhang Option In Star
updated 8 months ago by
Kermit
▴ 90 • written 10.1 years ago by
Martombo
★ 3.1k
298
votes
122
replies
32k
views
29 follow
Mean Length Of Fasta Sequences
code
fasta
sequence
codegolf
updated 6 months ago by
jena
▴ 290 • written 13.7 years ago by
Eric Normandeau
11k
78
votes
38
replies
32k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 27 days ago by
nickp60
▴ 60 • written 7.8 years ago by
andrew.j.skelton73
6.5k
48
votes
18
replies
32k
views
10 follow
How To Get Promoter Sequences For Human Genes?
promoter
sequence
human
genome
updated 4 months ago by
Ram
43k • written 13.9 years ago by
Yuri
★ 1.7k
20
votes
9
replies
32k
views
8 follow
Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
biomart
r
bioconductor
updated 10 months ago by
Kevin Blighe
87k • written 11.7 years ago by
sthait
▴ 120
36
votes
25
replies
32k
views
15 follow
Downsampling dataset with more than 60 million reads
next-gen
RNA-Seq
updated 3 months ago by
asalimih
▴ 60 • written 9.6 years ago by
mike
▴ 90
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 8 months ago by
amziepickles
• 0 • written 8.1 years ago by
Obi Griffith
20k
185
votes
45
replies
31k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline
general
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Giovanni M Dall'Olio
28k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner
snp
sequencing
updated 4 months ago by
Ram
43k • written 14.0 years ago by
Pierre Lindenbaum
160k
79
votes
86
replies
31k
views
20 follow
Tool:
Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify
storage
bbmap
pigz
compression
updated 9 months ago by
Ram
43k • written 7.3 years ago by
Brian Bushnell
20k
28
votes
16
replies
31k
views
11 follow
How Do I Convert From Bed Format To Gff Format?
gff
galaxy
bed
updated 5 months ago by
Ram
43k • written 14.5 years ago by
Istvan Albert
100k
103
votes
42
replies
30k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 20 days ago by
Jeremy Leipzig
22k • written 10.4 years ago by
14134125465346445
★ 3.6k
72
votes
71
replies
30k
views
17 follow
Tool:
EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot
bioconductor
ggplot2
ggrepel
updated 9 months ago by
Ram
43k • written 5.6 years ago by
Kevin Blighe
87k
14
votes
8
replies
30k
views
NarrowPeak format of ChiP-seq
ChIP-Seq
tag-density
updated 9 months ago by
minakshiboruahassam
• 0 • written 9.8 years ago by
liu4gre
▴ 210
4
votes
9
replies
30k
views
8 follow
How To Get Chromosome Position Given Rs Number?
snp
chromosome
position
updated 4 months ago by
GenoMax
140k • written 10.4 years ago by
chrismas05
• 0
130
votes
19
replies
30k
views
9 follow
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
RNA-Seq
alignment
next-gen
R
assembly
updated 9 weeks ago by
Ram
43k • written 4.5 years ago by
WUSCHEL
▴ 750
23
votes
12
replies
30k
views
9 follow
Extract Alignment From Very Large Bam File
bam
updated 9 weeks ago by
Ram
43k • written 11.8 years ago by
Plantae
▴ 390
24
votes
11
replies
30k
views
9 follow
Bed For Agilent Sureselect All Exon Kits ?
bed
exome
agilent
next-gen
written 11.4 years ago by
Pierre Lindenbaum
160k
17
votes
14
replies
30k
views
13 follow
Merge Paired-End Reads
fastq
updated 11 months ago by
Ram
43k • written 12.5 years ago by
Nicolas Rosewick
10k
52
votes
15
replies
30k
views
10 follow
Where To Download Pam50 Gene Set?
cancer
annotation
classification
updated 8 months ago by
DareDevil
★ 4.3k • written 10.7 years ago by
user
▴ 940
14,233 results • Page
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Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your response. There was no particular reason of `LEADING:20 and TRAILING:20`, but I used the same parameters as I had used …
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
A significant fraction of your reads appear to have the nextera sequence, that combined to this directive `LEADING:20` (do you have a reaso…
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Here is my fastqc, especially adapter content graph, before trimming(R1 and R2): ![enter image description here][1] And this after trimm…
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thanks, I modified.
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160k
11 years ago: https://www.biostars.org/p/7126/
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★ 1.7k
haha yes exactly! After the first or second ruined fasta, I started "catting" all fasta files and piping to other commands, just to reduce …
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Istvan Albert
100k
... ha, beat me to it, posted at the same time ... this error rules them all .. here is a cool trick on how to count fasta headers in file…
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I've definitely ruined some genome fasta files by running `grep ^> mygenome.fasta` instead of `grep "^>" mygenome.fasta`
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o.nad
• 0
Hello. I faced the same problem but not able to resolve it. I don't have double quotation and no NA values and the dataset used is in the f…
Answer: Annotation of Complex genomes using NCBI Genome Workbench
by
Lissa Cruz Saavedra
• 0
Hi Recently, I used https://www.gensas.org/ to make the annotation. It was pretty practical and in my opinion easy. You just need to up…
Comment: Hybrid assembly Pacbio- Nanopore
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Lissa Cruz Saavedra
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Hi Thanks for your answer. I think I have very good coverage. My genome size is 48M. I also have data from poreC and illumina, the last on…
Comment: Variant calling of GBS data
by
analyst
▴ 10
Anyone please suggest which variant caller can be the best choice for variant calling of GBS data for polyploid plant.
Comment: Variant calling of GBS data
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analyst
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Does GATK Haplotypecaller take care of ploidy because few plants are polyploid?
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More than likely they will only be available in the accompanying analysis app (Explify RPIP) in BaseSpace. Check with Illumina tech support…
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Pretty sure I have done it, but can't remember the details. You know that thing about blocking out traumatic events ...
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