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1,157 results • Page 1 of 24
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98
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106
replies
46k
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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
362
votes
82
replies
143k
views
35 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
updated 23 days ago by ▴ 290 • written 11.2 years ago by ★ 4.4k
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq next-gen-sequencing
updated 21 days ago by 43k • written 12.8 years ago by ★ 1.8k
103
votes
42
replies
31k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 10 days ago by 22k • written 10.4 years ago by ★ 3.6k
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 9 days ago by • 0 • written 8.8 years ago by ▴ 170
10
votes
36
replies
5.8k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA batch-effect DESeq2 R
updated 2 days ago by 43k • written 5.7 years ago by ▴ 620
49
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 21 days ago by 100k • written 8.1 years ago by 43k
81
votes
27
replies
20k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq atac-seq normalization
updated 16 days ago by • 0 • written 4.3 years ago by ▴ 240
85
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 1 day ago by • 0 • written 3.5 years ago by 3.2k
23
votes
23
replies
9.8k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq removeBatchEffect batch-effect edger
updated 1 day ago by 43k • written 5.3 years ago by ▴ 130
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 2 days ago by 43k • written 6.8 years ago by ★ 1.3k
57
votes
22
replies
28k
views
7 follow
Batch correction in DESeq2
Combat DESeq2 Batch-Effect
updated 13 days ago by 43k • written 4.5 years ago by ▴ 510
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 9 days ago by 43k • written 5.0 years ago by ▴ 260
5
votes
20
replies
4.1k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 9 days ago by 43k • written 6.2 years ago by ▴ 90
7
votes
20
replies
6.3k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 7 days ago by ▴ 190 • written 4.3 years ago by ▴ 80
18
votes
20
replies
4.4k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray differential-gene-expression
updated 9 days ago by 43k • written 7.5 years ago by ▴ 80
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 15 hours ago by 43k • written 4.5 years ago by ★ 1.4k
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome phg_v2 plants PHG
17 days ago by b.contreras.moreira ▴ 160
12
votes
17
replies
6.0k
views
9 follow
ACMG assignment tools
wes acmg WES WGS
updated 15 days ago by • 0 • written 3.9 years ago by ▴ 180
6
votes
17
replies
6.5k
views
Can you add a label key to heatscatter plot in R?
heatscatter visualization R
updated 2 days ago by 43k • written 9.5 years ago by ▴ 100
3
votes
16
replies
2.7k
views
design matrix for dge
limma differential-gene-expression r
updated 9 days ago by 43k • written 7.9 years ago by ▴ 50
0
votes
16
replies
1.0k
views
What is the sequence origin in human plasma?
human sequence cfDNA
6 days ago by biwdpang • 0
17
votes
16
replies
14k
views
10 follow
How to extract the longest isoform from multi fasta file
perl extract fasta python isoform
updated 15 days ago by • 0 • written 9.7 years ago by ▴ 290
8
votes
16
replies
5.3k
views
9 follow
visualize CNV data based on WGS
CNV
updated 29 days ago by ▴ 50 • written 6.3 years ago by ★ 1.4k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 2 hours ago by ▴ 10 • written 10.2 years ago by ▴ 180
5
votes
15
replies
4.9k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq IGV mapping
updated 27 days ago by • 0 • written 4.8 years ago by ▴ 160
105
votes
15
replies
112k
views
16 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 29 days ago by ▴ 140 • written 11.9 years ago by 12k
4
votes
14
replies
4.7k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 22 days ago by 43k • written 22 months ago by ▴ 20
5
votes
14
replies
900
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications dorado basecalling nanopore methylation
updated 7 days ago by 141k • written 28 days ago by ▴ 20
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna rRNA metagenomics
updated 24 days ago by 43k • written 13.5 years ago by ▴ 650
12
votes
14
replies
2.4k
views
8 follow
Forum: Recovering bam files after unknown deletion in the storage
photorec bam sequencing
written 4.9 years ago by ▴ 70
22
votes
14
replies
28k
views
7 follow
removing batch effects using ComBat and SVA
SVA ComBat R Batch-effect
updated 10 days ago by 43k • written 7.9 years ago by ▴ 280
13
votes
13
replies
18k
views
9 follow
How Do I Translate Multiple (More Than 25000) Dna Sequences With Different Frames To Protein Seuquence?
dna protein
updated 10 days ago by • 0 • written 10.3 years ago by ▴ 170
12
votes
13
replies
4.4k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression RNA-Seq glm DESeq2
updated 9 days ago by 43k • written 6.2 years ago by ★ 1.6k
5
votes
13
replies
9.0k
views
8 follow
biomaRt: Timeout on getBM().
r biomart ensembl
updated 7 days ago by ★ 2.0k • written 2.8 years ago by ▴ 40
6
votes
13
replies
544
views
Allocating right resources to HPC using LSF scheduler
BWA GATK hpc lsf bsub
24 days ago by Maverick ▴ 10
4
votes
13
replies
766
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 2 days ago by ★ 1.7k • written 7 days ago by • 0
6
votes
13
replies
578
views
Variant calling of GBS data
GBS variants BQSR
21 days ago by analyst ▴ 20
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
1 day ago by Ram 43k
8
votes
12
replies
3.5k
views
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
ATAC-seq
updated 16 days ago by • 0 • written 3.4 years ago by ▴ 40
5
votes
12
replies
1.5k
views
Subbmission Data
RNA-seq
updated 16 days ago by 43k • written 14 months ago by ▴ 50
3
votes
12
replies
719
views
Facing problem with extracting phenotypic data from GEO
WGCNA GEO
22 days ago by bioinfo_enthusiast • 0
6
votes
12
replies
5.6k
views
6 follow
Getting sample information from GEO
GEO NCBI
updated 23 days ago by • 0 • written 6.9 years ago by ▴ 350
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 23 days ago by 43k • written 5.5 years ago by ▴ 110
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 16 hours ago by • 0 • written 12.0 years ago by ★ 2.9k
11
votes
12
replies
695
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 11 hours ago by 43k • written 17 hours ago by • 0
2
votes
12
replies
695
views
Nanopore data filtering using fastp
fastp nanopore
21 days ago by emilydolivo97 ▴ 10
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 3 days ago by 43k • written 4.0 years ago by ▴ 330
3
votes
12
replies
474
views
struggle to get fasta files from ucsc goldenPath
ucsc getfasta fasta
16 days ago by Lila M ★ 1.2k
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 1 day ago by 43k • written 4.9 years ago by ▴ 330
1,157 results • Page 1 of 24
Recent Votes
Answer: Ciriquant not configuring hisat2 indexed files
Answer: Ciriquant not configuring hisat2 indexed files
DNA Methylation: Sequencing Techniques
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Answer: Indexing the Reference Genome is not done in STAR
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
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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
Comment: Korean human genome reference file by SeoGyun • 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool by Ashok • 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo) by cmdcolin ★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB by 航太郎 • 0
Thanks for your guide!
Comment: Removing duplicates by joe ▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis by swbarnes2 14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file by swbarnes2 14k
Shouldn't you use PicardTools for this?
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