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1,000 results • Page 3 of 20
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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 37k • written 8.9 years ago by ★ 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 37k • written 12.9 years ago by ★ 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 37k • written 8.0 years ago by ▴ 920
9
votes
30
replies
9.4k
views
small RNA-seq pipelines
small-RNA-seq pipelines
updated 8 months ago by 37k • written 7.9 years ago by ▴ 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 37k • written 7.8 years ago by 18k
267
votes
29
replies
245k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 9 weeks ago by 37k • written 10.2 years ago by ▴ 610
136
votes
29
replies
6.4k
views
16 follow
How Do We Discourage Ad-Hoc Bioinformatic Analyses?
software
updated 9 months ago by 37k • written 12.1 years ago by 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 37k • written 9.6 years ago by ▴ 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 37k • written 11.8 years ago by ▴ 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 37k • written 8.2 years ago by ▴ 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 ▴ 620 • written 5.0 years ago by ▴ 490
61
votes
29
replies
6.3k
views
14 follow
Best bioinfo one-liners?
linux
updated 24 days ago by 37k • written 7.7 years ago by 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 37k • written 7.0 years ago by ▴ 40
6
votes
29
replies
1.8k
views
Column lengths differ error (ArchR)
atac-seq cellranger r archr
updated 7 months ago by 125k • written 7 months ago by • 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 125k • written 6.9 years ago by 20k
33
votes
28
replies
10k
views
9 follow
Is There Any Reference Exome ?
exome next-gen-sequencing
updated 7 weeks ago by 37k • written 11.8 years ago by 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 37k • written 8.0 years ago by ▴ 90
14
votes
28
replies
8.9k
views
11 follow
Split fastq according to barcodes
fastq demultiplexing scRNA-seq
updated 11 months ago by ▴ 50 • written 4.1 years ago by ▴ 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 37k • written 11.2 years ago by ★ 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 ★ 2.6k • written 10.6 years ago by ▴ 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 37k • written 10.0 years ago by ★ 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 ▴ 10 • written 4.2 years ago by ▴ 40
18
votes
28
replies
12k
views
8 follow
Subsample BAM to fixed number of alignments
subsampling bam
updated 4 weeks ago by 37k • written 7.6 years ago by ★ 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 37k • written 11.1 years ago by ▴ 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 37k • written 11.5 years ago by ★ 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 37k • written 7.0 years ago by ★ 2.4k
42
votes
27
replies
4.3k
views
12 follow
What Do You Think Microsoft Biology Foundation?
updated 3 months ago by 37k • written 11.7 years ago by ▴ 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 ▴ 70 • written 9.1 years ago by ▴ 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 37k • written 10.8 years ago by 33k
27
votes
27
replies
29k
views
10 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 6 months ago by ▴ 240 • written 11.5 years ago by ★ 1.7k
12
votes
26
replies
29k
views
getting intersect between two lists of genes in R
gene R
updated 6 months ago by 37k • written 7.3 years ago by ★ 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 37k • written 8.5 years ago by 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 37k • written 10.0 years ago by ▴ 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 37k • written 6.0 years ago by ▴ 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 37k • written 7.6 years ago by ★ 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 37k • written 9.0 years ago by 96k
34
votes
26
replies
14k
views
13 follow
Reliable Fastq compression programs
fastq compression reliability
updated 11 weeks ago by ▴ 240 • written 7.3 years ago by 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 152k • written 4.9 years ago by ▴ 160
25
votes
26
replies
2.9k
views
warning in R
R
updated 25 days ago by 37k • written 7.7 years ago by ★ 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 37k • written 7.0 years ago by ★ 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 37k • written 8.0 years ago by ▴ 960
38
votes
26
replies
9.7k
views
Remove optical duplicates from bam file
sequencing
updated 6 months ago by 37k • written 8.4 years ago by ▴ 510
6
votes
26
replies
4.1k
views
6 follow
Is there a limit for SAMTOOLS tview option?
alignment
updated 5 months ago by ▴ 130 • written 5.3 years ago by ▴ 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 37k • written 10.0 years ago by ▴ 110
72
votes
25
replies
94k
views
14 follow
How to count fastq reads
sequence next-gen fastq reads
updated 7 months ago by 37k • written 7.8 years ago by ▴ 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 37k • written 8.7 years ago by 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 37k • written 10.4 years ago by 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 37k • written 10.8 years ago by ★ 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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Recent Replies
Answer: Python Dictionary of Primer3-py Primer Designs by barslmn ★ 1.2k
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 by 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? by demoraesdiogo2017 ▴ 80
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 by samuel.a.odonnell ▴ 450
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 by 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 by Estefania ▴ 10
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 by rasing02 • 0
Thank you jared.andrews07
Comment: extracting input files form Seurat by rasing02 • 0
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 by GenoMax 125k
I don't think they have provided processed data as a single upload.
Answer: extracting input files form Seurat by jared.andrews07 ★ 14k
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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