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1,000 results • Page 5 of 20
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79
votes
16
replies
48k
views
11 follow
How do you cite a tool that doesn't have a publication?
citation academic style
updated 8.0 years ago by 23k • written 8.1 years ago by ★ 1.1k
30
votes
10
replies
48k
views
Filtering A Sam File For Quality Scores
sam
updated 12.0 years ago by 11k • written 12.0 years ago by ★ 1.3k
39
votes
14
replies
48k
views
7 follow
Extraction Of Header Of Sequences In Fasta File
perl fasta python parsing
updated 24 months ago by 54k • written 12.3 years ago by ▴ 350
3
votes
5
replies
48k
views
Convert text file to VCF file ?
vcf
updated 10 months ago by 43k • written 9.1 years ago by ▴ 280
24
votes
14
replies
47k
views
7 follow
Gene symbol convert to Entrez ID
Entrez R biomart
updated 5.6 years ago by 11k • written 6.9 years ago by ▴ 190
32
votes
8
replies
47k
views
7 follow
Difference Between "Pipeline" And "Workflow" ?
next-gen sequencing
written 12.2 years ago by ★ 1.5k
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq gene
updated 9 months ago by 43k • written 10.9 years ago by ▴ 250
6
votes
12
replies
47k
views
9 follow
Opening A Fasta File In Windows
fasta blast makeblastdb
updated 12.1 years ago by • 0 • written 12.1 years ago by • 0
22
votes
4
replies
47k
views
Convert plink files to VCF: Reference allele file
SNP genome
updated 18 months ago by 43k • written 8.7 years ago by ▴ 70
49
votes
4
replies
47k
views
How To Convert The Bed File To Ped File
bed ped
updated 19 months ago by • 0 • written 13.7 years ago by ▴ 310
112
votes
24
replies
47k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp samtools alignment next-gen sequencing
updated 19 months ago by 43k • written 12.9 years ago by ▴ 480
118
votes
74
replies
46k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 17 months ago by 141k • written 13.4 years ago by ★ 3.3k
77
votes
18
replies
46k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 20 months ago by • 0 • written 13.9 years ago by ★ 1.1k
57
votes
23
replies
46k
views
14 follow
Bam File: Change Chromosome Notation
samtools bam
updated 2.9 years ago by 11k • written 12.5 years ago by ▴ 160
117
votes
66
replies
46k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 13 months ago by 43k • written 5.8 years ago by 81k
98
votes
106
replies
46k
views
26 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 10 days ago by ▴ 20 • written 5.6 years ago by 87k
17
votes
5
replies
46k
views
Scale Data Before Drawing Heatmap Or Using Heatmap(..., Scale="Columan") In R?
heatmap r
updated 12.4 years ago by 54k • written 12.4 years ago by ▴ 140
11
votes
8
replies
45k
views
Converting Smiles To Iupac Chemical Name?
updated 11.8 years ago by 5.4k • written 11.8 years ago by ▴ 730
9
votes
12
replies
45k
views
8 follow
Tools to view fastq file
fastq
updated 9 months ago by 43k • written 8.0 years ago by ▴ 40
81
votes
6
replies
45k
views
6 follow
Read Group In Sam/Bam Files: What Do They Exactly Describe?
bam samtools next-gen
updated 2.1 years ago by 43k • written 12.0 years ago by 4.4k
49
votes
10
replies
45k
views
When and why is bwa aln better then bwa mem?
aln comparison bwa mem
updated 3.0 years ago by 43k • written 9.5 years ago by 14k
298
votes
27
replies
45k
views
33 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq sequencing papers
updated 21 months ago by 43k • written 8.2 years ago by ★ 2.4k
32
votes
7
replies
45k
views
6 follow
Using transcripts per million (TPM)
RNA-Seq deseq2 tpm
updated 21 months ago by 43k • written 9.1 years ago by ▴ 170
22
votes
7
replies
45k
views
Extracting cells only from one condition (Seurat)
single cell rnaseq seurat RNA-Seq R
updated 3.0 years ago by ▴ 50 • written 4.2 years ago by ▴ 380
30
votes
14
replies
45k
views
9 follow
Extracting Read Count For Each Gene/Exon From Rna-Seq Bam Files
rna-seq differential expression
updated 7.9 years ago by 20 • written 11.9 years ago by ▴ 310
34
votes
11
replies
44k
views
8 follow
Where Can I Download Some Bam Files?
bam RNA-seq
updated 3 months ago by 43k • written 11.9 years ago by ▴ 160
32
votes
11
replies
44k
views
9 follow
How To Sort Sam File
samtools sam
updated 15 months ago by 43k • written 10.2 years ago by ★ 1.1k
134
votes
27
replies
44k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 24 months ago by 43k • written 12.0 years ago by 33k
17
votes
3
replies
44k
views
What'S The Meaning Of "Bridge Pcr" In The Next Generation Sequencing
pcr sequencing
updated 10.8 years ago by ★ 5.3k • written 10.8 years ago by ▴ 130
25
votes
23
replies
44k
views
12 follow
How To Generate A Consensus Fasta Sequence From Sam Tools Pileup?
samtools next-gen sequencing fasta
updated 10.2 years ago by ▴ 180 • written 13.9 years ago by 18k
5
votes
3
replies
44k
views
Extract the values by matching two rows of one dataframe with the two columns of another dataframe
dataframe match
updated 23 months ago by 43k • written 9.1 years ago by ★ 2.1k
63
votes
8
replies
44k
views
6 follow
Why Do You Need To Use Cdna For Rna-Seq?
rna-seq cdna
updated 7.7 years ago by • 0 • written 11.5 years ago by ▴ 460
23
votes
8
replies
44k
views
Convert .Txt File To Bed File
bed
updated 9.8 years ago by ▴ 260 • written 12.6 years ago by ★ 1.7k
32
votes
10
replies
44k
views
8 follow
Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
tophat illumina strand
updated 18 months ago by 43k • written 11.2 years ago by 10k
25
votes
9
replies
44k
views
Converting Gff To Bed With Bedtools?
gff bed bedtools
updated 10 weeks ago by 43k • written 11.2 years ago by ▴ 940
112
votes
56
replies
44k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 19 months ago by 43k • written 11.9 years ago by ▴ 380
32
votes
5
replies
44k
views
What is Differential Expression?
DNA genes
updated 2.3 years ago by 43k • written 9.7 years ago by ▴ 50
85
votes
19
replies
44k
views
17 follow
How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
assembly quality next-gen
updated 2.2 years ago by ▴ 10 • written 11.2 years ago by ▴ 470
3
votes
5
replies
44k
views
how to set the size of cell of heatmap.2 in R
heatmap.2 R
updated 2.1 years ago by 43k • written 9.4 years ago by ★ 2.2k
53
votes
19
replies
43k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 14 months ago by 43k • written 12.0 years ago by 11k
9
votes
7
replies
43k
views
R programming: compare columns to column and get the mismatch
R
updated 14 months ago by 43k • written 9.0 years ago by ★ 2.1k
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 6 months ago by ▴ 130 • written 7.8 years ago by ★ 5.3k
37
votes
15
replies
43k
views
8 follow
FPKM vs raw counts vs RPKM
counts rpkm raw fpkm RNA-Seq
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 360
26
votes
9
replies
43k
views
How Logfc Value Is Calculated In Edger?
edger r RNA-seq
updated 13 months ago by 43k • written 10.5 years ago by ▴ 240
60
votes
52
replies
43k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 13 months ago by 43k • written 7.6 years ago by ★ 3.5k
14
votes
6
replies
43k
views
Does Anyone Know How To Cite Ncbi Wwwblast In A Manuscript?
ncbi
updated 10.7 years ago by ▴ 180 • written 10.7 years ago by ▴ 830
48
votes
9
replies
43k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 11 weeks ago by ▴ 640 • written 7.5 years ago by ▴ 570
121
votes
35
replies
43k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 11 months ago by 43k • written 6.8 years ago by ▴ 810
25
votes
6
replies
43k
views
Aggregate multiple rows based on common values in given columns
R
updated 5.6 years ago by 11k • written 8.4 years ago by ▴ 70
63
votes
16
replies
43k
views
11 follow
How To Analyze Imputed Gwas Data
gwas r snp imputation plink
updated 3.8 years ago by ▴ 70 • written 13.1 years ago by 2.8k
1,000 results • Page 5 of 20
Recent Votes
Answer: Problem with Sniffles pipeline and SV calling help
Illumina reads preprocessing best practice for snp calling applications
Comment: Illumina reads preprocessing best practice for snp calling applications
Installing/switching between versions of R/Rstudio/Bioconductor
How To Generate Phylogeny Tree, Based On Snps?
How To Construct Phylogenetic Tree Using Snps
Basic normalization, batch correction and visualization of RNA-seq data
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Popular Question to DanielEB_fisk ▴ 20
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Recent Replies
Comment: Illumina reads preprocessing best practice for snp calling applications by Enrique • 0
Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
Comment: Could you please assist in identifying this cluster? by ATpoint 81k
The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
Comment: Free/open source 23andme-like analysis by joe ▴ 510
Thank you, I added 'accurate' now ;) I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
Comment: Memory usage of picard Samsort by ATpoint 81k
Guys, just use `samtools sort` which won't get you into trouble with any of that.
Comment: Ciriquant not configuring hisat2 indexed files by Carlo Yague 8.6k
I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the…
Answer: Memory usage of picard Samsort by tamas.malkocs • 0
For me, setting `TMP_DIR` (`--TMP_DIR /home/tmp`) didn't work in picard 2.21.1. What solved the issue was setting the environmental variabl…
Answer: Plink merge errors. by Dinmukhamed • 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files by Atul K. • 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file by Maria • 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis by Michael 54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi by Pierre Lindenbaum 161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi by b.contreras.moreira ▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software by colindaven 6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam by Hagen ▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably by Kai Xin • 0
will look into that. Thank you very much
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