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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
17
votes
30
replies
28k
views
8 follow
Getting A Vcf File From A Fasta Alignment
vcf
fasta
conversion
alignment
updated 9 months ago by
Ram
37k • written 8.9 years ago by
Bioch'Ti
★ 1.1k
102
votes
30
replies
59k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
tool
updated 7 months ago by
Ram
37k • written 12.9 years ago by
Biostar User
★ 1.0k
15
votes
30
replies
2.7k
views
how to retrieve specific raws from a data matrix based on Affymetrix ID in Linux
affymetrix
linux
matrix
updated 9 months ago by
Ram
37k • written 8.0 years ago by
Mo
▴ 920
9
votes
30
replies
9.4k
views
small RNA-seq pipelines
small-RNA-seq
pipelines
updated 8 months ago by
Ram
37k • written 7.9 years ago by
Saad Khan
▴ 410
83
votes
30
replies
5.4k
views
18 follow
Forum:
Optimal design for bioinformatics "lab" space?
design
lab-space
updated 7 months ago by
Ram
37k • written 7.8 years ago by
Casey Bergman
18k
267
votes
29
replies
245k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 9 weeks ago by
Ram
37k • written 10.2 years ago by
sohadb1357
▴ 610
136
votes
29
replies
6.4k
views
16 follow
How Do We Discourage Ad-Hoc Bioinformatic Analyses?
software
updated 9 months ago by
Ram
37k • written 12.1 years ago by
Jeremy Leipzig
21k
33
votes
29
replies
18k
views
12 follow
Large File Transfers Of Ngs Data: Rsync / Bbcp / Unison / What?
data
updated 5 weeks ago by
Ram
37k • written 9.6 years ago by
Dan Sheppard
▴ 110
34
votes
29
replies
30k
views
10 follow
Downloading And Maintaining A Local, Blast-Able Nr Database
ncbi
database
blast
installation
updated 8 months ago by
Ram
37k • written 11.8 years ago by
Anjan
▴ 830
18
votes
29
replies
15k
views
7 follow
What is the best way to match gene id with gene name.
RNA-Seq
R
updated 11 months ago by
Ram
37k • written 8.2 years ago by
M K
▴ 590
49
votes
29
replies
9.7k
views
7 follow
How to get sample names and genotype for SNP in multi-sample VCF file
SNP
genotype
GATK
updated 10 months ago by
User000
▴ 620 • written 5.0 years ago by
hellbio
▴ 490
61
votes
29
replies
6.3k
views
14 follow
Best bioinfo one-liners?
linux
updated 24 days ago by
Ram
37k • written 7.7 years ago by
Manu Prestat
4.1k
29
votes
29
replies
2.4k
views
6 follow
Tool:
weld (former brew) - yet another fastq utility
illlumina
python
updated 6 months ago by
Ram
37k • written 7.0 years ago by
tinysnippets
▴ 40
6
votes
29
replies
1.8k
views
Column lengths differ error (ArchR)
atac-seq
cellranger
r
archr
updated 7 months ago by
GenoMax
125k • written 7 months ago by
bioinformatics.girl
• 0
82
votes
28
replies
27k
views
19 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
GenVisR
BioConductor
R
Graphics
Tutorial
updated 12 weeks ago by
GenoMax
125k • written 6.9 years ago by
Obi Griffith
20k
33
votes
28
replies
10k
views
9 follow
Is There Any Reference Exome ?
exome
next-gen-sequencing
updated 7 weeks ago by
Ram
37k • written 11.8 years ago by
Khader Shameer
18k
72
votes
28
replies
5.1k
views
10 follow
Forum:
Bioinformatics commercial services as a risk factor for scientific misconduct
commercial-services
ethics
misconduct
updated 7 months ago by
Ram
37k • written 8.0 years ago by
Angle45
▴ 90
14
votes
28
replies
8.9k
views
11 follow
Split fastq according to barcodes
fastq
demultiplexing
scRNA-seq
updated 11 months ago by
camelest
▴ 50 • written 4.1 years ago by
Hughie
▴ 30
38
votes
28
replies
15k
views
11 follow
Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Interface?
galaxy
command-line
updated 8 months ago by
Ram
37k • written 11.2 years ago by
Samuel Lampa
★ 1.3k
16
votes
28
replies
21k
views
15 follow
Extract Base Based On Position From Bam File
mpileup
samtools
updated 6 months ago by
Prakki Rama
★ 2.6k • written 10.6 years ago by
Empyrean
▴ 160
30
votes
28
replies
14k
views
6 follow
Split Read Mapping By Bwa And Bowtie2
mapping
sequencing
bwa
bowtie2
updated 10 months ago by
Ram
37k • written 10.0 years ago by
Abhi
★ 1.6k
3
votes
28
replies
7.7k
views
WGCNA soft thresholding problem
WGCNA
RNA-Seq
soft thresholding
data normalization
updated 11 months ago by
ChengZ
▴ 10 • written 4.2 years ago by
catagui
▴ 40
18
votes
28
replies
12k
views
8 follow
Subsample BAM to fixed number of alignments
subsampling
bam
updated 4 weeks ago by
Ram
37k • written 7.6 years ago by
Daniel
★ 3.9k
18
votes
27
replies
16k
views
20 follow
Where Can I Download Vcf Files For Publicly Available Data?
snp
vcf
download
updated 7 months ago by
Ram
37k • written 11.1 years ago by
Kevin
▴ 640
60
votes
27
replies
25k
views
18 follow
Links To Good Next Gen Sequence Analysis Training Courses And Centres
next-gen
sequencing
analysis
workshops
training
updated 10 months ago by
Ram
37k • written 11.5 years ago by
Travis
★ 2.8k
38
votes
27
replies
8.8k
views
10 follow
How Much Does It Cost To Align A Flowcell In The Cloud?
cloud
12 months ago by
Jeremy Leipzig
21k
292
votes
27
replies
41k
views
33 follow
Forum:
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq
sequencing
papers
updated 6 months ago by
Ram
37k • written 7.0 years ago by
CandiceChuDVM
★ 2.4k
42
votes
27
replies
4.3k
views
12 follow
What Do You Think Microsoft Biology Foundation?
updated 3 months ago by
Ram
37k • written 11.7 years ago by
Sirus
▴ 820
77
votes
27
replies
48k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 5 months ago by
Johan Zicola
▴ 70 • written 9.1 years ago by
Ram
▴ 180
131
votes
27
replies
40k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 9 months ago by
Ram
37k • written 10.8 years ago by
lh3
33k
27
votes
27
replies
29k
views
10 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 6 months ago by
opplatek
▴ 240 • written 11.5 years ago by
Bioscientist
★ 1.7k
12
votes
26
replies
29k
views
getting intersect between two lists of genes in R
gene
R
updated 6 months ago by
Ram
37k • written 7.3 years ago by
fi1d18
★ 4.1k
24
votes
26
replies
2.3k
views
Tool:
ClinCNV: CNV detection from short reads
cnv
calling
cna
Tool
variant
7 months ago by
German.M.Demidov
★ 2.9k
5
votes
26
replies
5.9k
views
Pre-computed list of genes in LD with a SNP with r2 from 1000Genomes / hg19
genomics
snp
ld
updated 5 weeks ago by
Ram
37k • written 8.5 years ago by
Khader Shameer
18k
105
votes
26
replies
38k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 4 months ago by
Ram
37k • written 10.0 years ago by
henryvuong
▴ 810
16
votes
26
replies
14k
views
16 follow
bedtools coverage gives error received illegal bin number, but that number isn't in my data!
ChIP-Seq
bedtools
updated 11 days ago by
Ram
37k • written 6.0 years ago by
tara.alpert
▴ 30
8
votes
26
replies
3.5k
views
Fasta sequence replacement based on header name
alignment
Assembly
sequencing
RNA-Seq
updated 6 weeks ago by
Ram
37k • written 7.6 years ago by
seta
★ 1.7k
68
votes
26
replies
24k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
rna-seq
tutorial
Tutorial
updated 6 days ago by
Ram
37k • written 9.0 years ago by
Istvan Albert
96k
34
votes
26
replies
14k
views
13 follow
Reliable Fastq compression programs
fastq
compression
reliability
updated 11 weeks ago by
jena
▴ 240 • written 7.3 years ago by
Eric Normandeau
11k
20
votes
26
replies
4.8k
views
9 follow
Is there a better tool for visualizing your variants after annotation than Excel?
annotations
variants
updated 5 months ago by
Pierre Lindenbaum
152k • written 4.9 years ago by
Tania
▴ 160
25
votes
26
replies
2.9k
views
warning in R
R
updated 25 days ago by
Ram
37k • written 7.7 years ago by
fi1d18
★ 4.1k
26
votes
26
replies
3.3k
views
Are my RNA-seq datasets strand-specific?
alignment
next-gen-sequencing
RNA-Seq
updated 6 months ago by
Ram
37k • written 7.0 years ago by
fi1d18
★ 4.1k
15
votes
26
replies
4.4k
views
How to interpret the result of GO analysis using Ontologizer / mapping GO IDs to GO TERMS ?
gene-ontology
R
RNA-Seq
updated 9 months ago by
Ram
37k • written 8.0 years ago by
jack
▴ 960
38
votes
26
replies
9.7k
views
Remove optical duplicates from bam file
sequencing
updated 6 months ago by
Ram
37k • written 8.4 years ago by
Anna S
▴ 510
6
votes
26
replies
4.1k
views
6 follow
Is there a limit for SAMTOOLS tview option?
alignment
updated 5 months ago by
jkim
▴ 130 • written 5.3 years ago by
bioplanet
▴ 60
31
votes
26
replies
7.9k
views
12 follow
How To Discard Sequences Longer Than N Nucleotides ?
small
rna
data
updated 4 months ago by
Ram
37k • written 10.0 years ago by
2011101101
▴ 110
72
votes
25
replies
94k
views
14 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 7 months ago by
Ram
37k • written 7.8 years ago by
Chenglin
▴ 250
7
votes
25
replies
9.3k
views
6 follow
Tool:
MIGEC: towards error-free profiling of immune repertoires
sequencing-error
tcr
molecular-barcode
antibody
Tool
updated 3 months ago by
Ram
37k • written 8.7 years ago by
mikhail.shugay
3.5k
94
votes
25
replies
31k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
fastq
trimming
qc
tutorial
Tutorial
updated 7 hours ago by
Ram
37k • written 10.4 years ago by
Istvan Albert
96k
136
votes
25
replies
74k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 10 months ago by
Ram
37k • written 10.8 years ago by
Ying W
★ 4.2k
1,000 results • Page
3 of 20
Recent Votes
Answer: Looking for a tool which provides mapping quality score distributions from BAM f
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: Gviz python alternative
Answer: Gviz python alternative
Answer: Annotating snps with gene information
Comment: Plotting Correlation matrix
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Answer: Python Dictionary of Primer3-py Primer Designs
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You're so close. You can simply loop over sequence dictionaries like you did with the `design_output` and check if the keys with `startswit…
Comment: Unable to install clusterProfiler on Mac M1
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GenoMax
125k
Have you installed `Xcode` and the command line tools that go with? If not you will need to install those.
Answer: SRA taxonomy analysis
by
Steve
• 0
Thanks @genomax I created an aws glue crawler to pull the data from s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/ I wonder if it …
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives?
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thanks! however, shouldn't it also have a gtf/gff file with the annotations?
Comment: Getting a VCF file from plink .bed, .fam and .bim files
by
hi.there
• 0
Thanks Ram. Yes. I have read all of this documentation before. --file and --bfile. I have actually tried doing the complete liftover be…
Answer: SRA taxonomy analysis
by
GenoMax
125k
This data may only be available using `BigQuery` for [**SRA in cloud**][1]. For more information on querying: https://www.ncbi.nlm.nih.g…
Comment: MesKit error message - Join columns must be present in data.
by
CH1374
• 0
column names for the maf are: [1] "Hugo_Symbol" "Chromosome" "Start_Position" [4] "End_Position" "Variant_Classification" "Variant_Type" [7…
Answer: scaffold assembly inro chromosomal assembly using reference genome
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Have a look at ragtag and ragout. I use ragout for smaller assemblies (~20 Mb and less) and ragtag for larger genomes.
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl
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Ram
37k
I've been meaning to work on a Biostars-specific code formatting manual for a while now but the basic is pretty simple: You can use backtic…
Comment: Multiline Fasta To Single Line Fasta
by
Onur
• 0
Thank you it's also worked for me too. Best,
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl
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Estefania
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Thanks Ram. Could you point to a manual on how to make the post look like yours? I just copy-pasted my R script and this is how it shows in…
Comment: extracting input files form Seurat
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rasing02
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Thank you jared.andrews07
Comment: extracting input files form Seurat
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rasing02
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Yes, I just need the input data so that investigators can use tools other than R to visualize the data in form of viloin plots or feature p…
Comment: Downloading 450k methylation data from GEO
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I don't think they have provided processed data as a single upload.
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You can get the data behind any of the plots easily enough: ``` p <- VlnPlot(Seurat_object, features = "X", group.by = "Names",split.by…
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