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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
226
votes
39
replies
288k
views
33 follow
Gene Id Conversion Tool
david
updated 6 months ago by
Ram
43k • written 14.5 years ago by
Renee
▴ 620
332
votes
92
replies
239k
views
58 follow
Tools To Calculate Average Coverage For A Bam File?
coverage
bam
sequencing
updated 8 months ago by
kalavattam
▴ 190 • written 13.3 years ago by
Biomed
5.0k
120
votes
31
replies
199k
views
17 follow
Correct Way To Parse A Fasta File In Python
python
fasta
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
124
votes
13
replies
174k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 7 months ago by
Ram
43k • written 13.8 years ago by
Biomed
5.0k
143
votes
14
replies
169k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
231
votes
38
replies
146k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 10 months ago by
Ram
43k • written 11.2 years ago by
Malachi Griffith
19k
362
votes
82
replies
144k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 4 weeks ago by
jena
▴ 290 • written 11.2 years ago by
ole.tange
★ 4.4k
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
147
votes
31
replies
137k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 9 months ago by
Ram
43k • written 12.2 years ago by
Anima Mundi
★ 2.9k
68
votes
18
replies
130k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing
samtools
updated 3 months ago by
Pierre Lindenbaum
161k • written 9.6 years ago by
Kizuna
▴ 870
76
votes
26
replies
120k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 5 months ago by
cschu181
★ 2.8k • written 9.0 years ago by
Chenglin
▴ 260
103
votes
34
replies
113k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 3 months ago by
Ram
43k • written 11.9 years ago by
GPR
▴ 390
105
votes
15
replies
112k
views
16 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 5 weeks ago by
xiaoleiusc
▴ 140 • written 11.9 years ago by
GouthamAtla
12k
124
votes
56
replies
103k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 6 months ago by
William
▴ 30 • written 9.9 years ago by
kay
▴ 370
171
votes
41
replies
98k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 7 months ago by
Ram
43k • written 12.9 years ago by
Palu
▴ 250
239
votes
176
replies
95k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 11 months ago by
Ram
43k • written 8.7 years ago by
TriS
★ 4.7k
105
votes
31
replies
94k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 4 months ago by
mmfansler
▴ 450 • written 12.8 years ago by
2184687-1231-83-
★ 5.1k
97
votes
19
replies
94k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
ucsc
fasta
sequence
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
93
votes
23
replies
92k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 3 months ago by
clara.apicella
• 0 • written 5.8 years ago by
otwtgin2010
▴ 610
103
votes
27
replies
89k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 11 months ago by
NIRJHAR
• 0 • written 11.9 years ago by
Rubal7
▴ 830
163
votes
64
replies
87k
views
39 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 3 months ago by
Ram
43k • written 13.1 years ago by
Ketil
4.1k
19
votes
14
replies
86k
views
10 follow
BLAST Database error: No alias or index file found for nucleotide database
blast
blastn
sift
makeblastdb
updated 6 months ago by
Ken
• 0 • written 9.5 years ago by
arronslacey
▴ 320
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 5 weeks ago by
Michael
54k • written 14.1 years ago by
Yuri
★ 1.7k
364
votes
58
replies
69k
views
44 follow
Forum:
Recommend Your Favorite Bioinformatics Books
education
books
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Istvan Albert
100k
138
votes
22
replies
65k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene
LIMMA
edgeR
updated 10 months ago by
Kevin Blighe
87k • written 6.4 years ago by
Mike
★ 1.9k
328
votes
54
replies
64k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome
visualization
updated 5 months ago by
Ram
43k • written 14.1 years ago by
brentp
24k
159
votes
24
replies
62k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing
splicing
rna-seq
updated 10 months ago by
Ram
43k • written 11.2 years ago by
Nicolas Rosewick
11k
102
votes
30
replies
62k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Biostar User
★ 1.0k
164
votes
70
replies
61k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 4 weeks ago by
Ram
43k • written 12.8 years ago by
Panos
★ 1.8k
93
votes
19
replies
60k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 10 months ago by
Ram
43k • written 13.6 years ago by
Niek De Klein
★ 2.6k
17
votes
6
replies
59k
views
Turn Off Blast Search On Reverse Complement Strand In Blastn
blast
sequence
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Zhaorong
★ 1.4k
52
votes
8
replies
59k
views
7 follow
Subsampling Bam File With Samtools
bam
samtools
updated 3 months ago by
giulia.trauzzi
▴ 10 • written 10.8 years ago by
madbessoul
▴ 250
1.2k
votes
206
replies
59k
views
108 follow
Forum:
What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 11 months ago by
Raony Guimarães
★ 1.4k • written 13.1 years ago by
Jeremy Leipzig
22k
45
votes
9
replies
58k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen
RNA-Seq
single-cell
R
updated 8 months ago by
camillab.
▴ 160 • written 4.4 years ago by
Payal
▴ 160
28
votes
22
replies
57k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r
genomics
entrez
updated 10 months ago by
cwang3444
• 0 • written 11.0 years ago by
grosy
▴ 90
50
votes
13
replies
57k
views
13 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 7 months ago by
camillab.
▴ 160 • written 8.3 years ago by
nash.claire
▴ 490
61
votes
23
replies
57k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam
mapping
updated 5 months ago by
Lluís R.
★ 1.2k • written 11.2 years ago by
Jordan
★ 1.3k
66
votes
19
replies
50k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 10 months ago by
Ram
43k • written 11.2 years ago by
14134125465346445
★ 3.6k
149
votes
70
replies
50k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 8 months ago by
Raheleh
▴ 260 • written 6.4 years ago by
Kevin Blighe
87k
56
votes
52
replies
50k
views
12 follow
Tool:
Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF
Gene-Clustering
updated 10 months ago by
Ram
43k • written 9.7 years ago by
EagleEye
7.5k
66
votes
23
replies
49k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 5 weeks ago by
Getnet Tesfaw
• 0 • written 6.4 years ago by
1769mkc
★ 1.2k
52
votes
21
replies
49k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 10 months ago by
Ram
43k • written 12.1 years ago by
Geparada
★ 1.5k
71
votes
15
replies
49k
views
10 follow
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
risk
minor
major
reference
alleles
written 6.0 years ago by
m98
▴ 420
3
votes
5
replies
48k
views
Convert text file to VCF file ?
vcf
updated 10 months ago by
Ram
43k • written 9.2 years ago by
CrazyB
▴ 280
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq
gene
updated 9 months ago by
Ram
43k • written 10.9 years ago by
hicsuntdrac0nis
▴ 250
98
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 18 days ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
87k
9
votes
12
replies
46k
views
8 follow
Tools to view fastq file
fastq
updated 10 months ago by
Ram
43k • written 8.0 years ago by
Roden Luo
▴ 40
34
votes
11
replies
45k
views
8 follow
Where Can I Download Some Bam Files?
bam
RNA-seq
updated 4 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 11 weeks ago by
Ram
43k • written 11.3 years ago by
user
▴ 940
35
votes
14
replies
44k
views
9 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf
bcftools
updated 6 months ago by
ashotmarg2004
▴ 130 • written 7.8 years ago by
William
★ 5.3k
1,000 results • Page
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Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
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Answer: gvcf joint calling
Answer: Heatmap and rna-seq
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Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
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▴ 710
Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
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6.4k
I used to use nextflow in a conda env. That requires the env to be active when a pipeline is started. Also I have productive pipelines whic…
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by
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just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
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by
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★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
Comment: ScRNA data question
by
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features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
Comment: gvcf joint calling
by
zihanss
• 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
Comment: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Guille
• 0
Thank you for your answer! The MDS plot seems to group most treatment groups close-by, so I'm starting to suspect the effect of treatment …
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
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Mensur Dlakic
★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq
by
dsull
★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
Gordon Smyth
★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
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Gordon Smyth
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The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu
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There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
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▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
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