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121,919 results • Page 709 of 2439
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5
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6
replies
1.9k
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How to install R in WinSCP server
R
updated 4.6 years ago by ★ 1.6k • written 4.6 years ago by ▴ 20
2
votes
1
reply
2.1k
views
What are the best scATAC-seq computational pipelines / tools / literature currently available?
single-cell scATAC-seq ATAC-seq pipeline
4.6 years ago by Sergio Martínez Cuesta ▴ 230
2
votes
4
replies
1.8k
views
Finding Fragment Size chip-seq paired end reads
ChIP-Seq sequencing
4.6 years ago by luckysardar171 ▴ 20
1
vote
0
replies
2.6k
views
fitting model to a read coverage spectra
genome k-mer spectra read coverage
updated 4.6 years ago by 20 • written 8.4 years ago by 16k
0
votes
0
replies
1.7k
views
Tool: I made QMplot: a python library and tools of generating high-quality manhattan and Q-Q plots for GWAS data
visualization Manhattan-Plot GWAS genome Python
updated 2.3 years ago by 45k • written 4.6 years ago by • 0
2
votes
1
reply
933
views
module vs miniconda in HPC
module miniconda conda HPC
4.6 years ago by Friyunnwoo ▴ 20
0
votes
3
replies
915
views
Fisher exact test for 2 by 20000 table and for 4 by 20000 table
gene
4.6 years ago by Rob ▴ 180
2
votes
1
reply
1.1k
views
bcftools command not working
bcftools dna-seq SNP
updated 4.6 years ago by 153k • written 4.6 years ago by ▴ 30
4
votes
4
replies
4.6k
views
How do I use FindAllMarkers after making additional cluster assignments?
Seurat R single cell-RNA seq scRNA-seq
4.6 years ago by Pratik ★ 1.1k
1
vote
1
reply
1.2k
views
FastQC per base to total base calculator
FastQC MultiQC GC% N-content
4.6 years ago by jimmy0958073736 ▴ 40
2
votes
4
replies
3.7k
views
Pharmgkb: Obtain A List Of Vip Genes And List All Linked Drugs To Them
pharmgkb
updated 4.6 years ago by 45k • written 13.5 years ago by ▴ 100
0
votes
1
reply
667
views
Downloading multiple studies SRA data through while loop
e-utilities
4.6 years ago by jobrien20 • 0
0
votes
2
replies
704
views
finding bacterial genes in dataset
microbiome gene sequencing
4.6 years ago by john.chandler2011 • 0
0
votes
0
replies
887
views
Cluster Stability Assesment
rna-seq Seurat clustering R
4.6 years ago by Maria17 ▴ 40
0
votes
4
replies
1.3k
views
Bacterial refseq to remove contaminats
transcritpome RNA-seq
updated 4.6 years ago by • 0 • written 4.6 years ago by ▴ 110
1
vote
5
replies
2.5k
views
SRA toolkit fastq files download error
RNA-Seq SRA
4.6 years ago by sidrah.maryam ▴ 70
0
votes
0
replies
935
views
kallisto preprocessing-Error: unspliced. bus has no BUS records
kallisto RNA-Seq bustools
updated 2.3 years ago by 45k • written 4.6 years ago by • 0
0
votes
3
replies
1.0k
views
Very small quantity of adapter contamination, real or not?
next-gen DNA-seq Quality control Adapters
4.6 years ago by Ismaelrymy • 0
0
votes
2
replies
1.9k
views
Extract unmapped sequenced from a sam file output from minimap2
get unmapped reads from sam file
updated 4.6 years ago by 13k • written 4.6 years ago by • 0
4
votes
2
replies
1.6k
views
Help with Mr Bayes parameters for 16S phylogeny
sequence Assembly mrbayes
4.6 years ago by buhbs ▴ 30
0
votes
5
replies
3.2k
views
Multi-factor time series design model in DESeq2 analysis
RNA-Seq
updated 2.9 years ago by 45k • written 10.2 years ago by • 0
2
votes
3
replies
1.9k
views
Short sequence alignment using Minimap2
assembly minimap2 kmer gRNA pacbio
updated 4.5 years ago by 153k • written 4.6 years ago by ▴ 10
2
votes
1
reply
756
views
Collapse bed and only sum overlapping parts
bed RNA-Seq alignment
4.6 years ago by Matthias ▴ 30
1
vote
1
reply
674
views
Rna-seq time series dataset
RNA-Seq next-gen
updated 4.6 years ago by 153k • written 4.6 years ago by • 0
8
votes
10
replies
2.2k
views
Forward and reverse single cell data analysis
RNA-Seq
updated 4.6 years ago by 15k • written 4.6 years ago by ▴ 260
3
votes
9
replies
5.5k
views
6 follow
Multiple ensembl gene ID for the same gene name (Symbol), how to deal with this while differential analysis?
RNA-Seq alignment next-gen ensembl
updated 3.4 years ago by ▴ 10 • written 4.6 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Web-based tool for 3D visualization of proteins given a .pbd file
protein 3D structure prediction
4.6 years ago by giusdalt95 ▴ 10
3
votes
8
replies
2.2k
views
How to find the secreted protein tags
RNA-Seq protein rna-seq R next-gen
updated 4.6 years ago by ★ 2.4k • written 4.6 years ago by ▴ 70
0
votes
4
replies
1.2k
views
How to solve the problem related to unmatched chromosome identifiers?
RNA-Seq
updated 4.6 years ago by 20 • written 4.7 years ago by ▴ 10
1
vote
0
replies
738
views
Compare the output of two MEME analyses
meme motif analysis
4.6 years ago by lessismore ★ 1.4k
4
votes
3
replies
824
views
Remove a row if two specific columns have similar/share contents
SNP next-gen
4.6 years ago by waqasnayab ▴ 250
1
vote
2
replies
825
views
question regarding QC of scRNA-seq data
scRNA-seq scRNA-seq QC
4.6 years ago by Alex V. Gopanenko • 0
0
votes
11
replies
2.5k
views
The pruned in file by bcftools gives error "Wrong VCF header" while calculating kinship matrix using Rvtests
software error
4.6 years ago by AVA ▴ 40
2
votes
3
replies
1.2k
views
Affymatrix microarray data do not have normal distribution after normalization (left skewed)
microarray R
updated 4.6 years ago by 89k • written 4.6 years ago by ▴ 30
16
votes
11
replies
2.6k
views
10 follow
Forum: Suggest common programming tasks for biologists who are novice programmers
education
updated 2.5 years ago by 45k • written 4.6 years ago by ▴ 40
4
votes
3
replies
4.3k
views
counting after aligning miRNA reads to miRBase mature miRNA instead of reference genome
miRNA-seq
updated 4.6 years ago by ▴ 160 • written 7.5 years ago by ▴ 30
0
votes
0
replies
544
views
Can I differenciate between two variants of the same plant spicies with NGS?
snp genome
4.6 years ago by jomagrax ▴ 40
1
vote
4
replies
939
views
question regarding histone and lncRNA genes in poly(A) RNA-seq data
rna-seq polyA rna-seq
4.6 years ago by Alex V. Gopanenko • 0
1
vote
11
replies
4.6k
views
How to get REF and ALT alleles from a genotype data?
snp genome R sequencing
updated 4.6 years ago by 24k • written 4.6 years ago by ▴ 10
0
votes
0
replies
597
views
Horizontal sub-windows for IGV
IGV bam
4.6 years ago by German.M.Demidov ★ 3.0k
1
vote
6
replies
1.1k
views
How can I locate a specific nucleotide based on a bam file?
alignment genome sequence
4.6 years ago by 2689563392 • 0
1
vote
4
replies
2.8k
views
LImma design matrix and contrast matrix creation
R limma gordon smyth
updated 4.6 years ago by ★ 2.1k • written 4.6 years ago by ▴ 10
0
votes
1
reply
893
views
error in processing Agilent two channel microarray raw data
microarray
updated 4.6 years ago by ★ 8.3k • written 4.6 years ago by ▴ 30
1
vote
1
reply
1.4k
views
interaction analysis of smallRNA-seq and RNA-seq data
srnaRNA-se RNA-Seq
updated 4.6 years ago by 20 • written 7.4 years ago by ▴ 150
3
votes
2
replies
1.3k
views
Retrieve initial query in getBM()
getBM biomaRt R gene
updated 17 months ago by 45k • written 4.6 years ago by • 0
0
votes
5
replies
4.8k
views
Is there any method to convert a text file to VCF format?
SNP R gene next-gen
updated 15 months ago by 45k • written 4.6 years ago by ▴ 20
0
votes
0
replies
668
views
Variant splicing position on CDS
SNV
4.6 years ago by heureuse ▴ 10
5
votes
8
replies
1.7k
views
Does the countToFPKM package work for single end RNA seq or its only for paired end?
RNA-Seq
updated 4.6 years ago by 11k • written 4.6 years ago by ▴ 10
0
votes
0
replies
887
views
Comparation hmmer vs blast
hmmer Blast comparation
4.6 years ago by zion22 ▴ 70
0
votes
0
replies
896
views
Stacks: Denovo.pl M, m and n paramters
Assembly SNP RAD-Seq Stacks
4.6 years ago by virtualinterlect • 0
121,919 results • Page 709 of 2439
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A: Binning Over Genes And Calculating The Coverage [Bedops/Bedmap]
Answer: [vg giraffe] Unable to add read group to BAM file
Comment: [vg giraffe] Unable to add read group to BAM file
Answer: [vg giraffe] Unable to add read group to BAM file
Answer: vcf multisample
Answer: vcf multisample
Answer: vcf multisample
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Recent Replies
Comment: Help with species tree with orthofinder, iqtree and branch labeling by GenoMax 153k
> I don’t have clear species labels in my headers, only sequence IDs. I have not used iqtree, so this is only a thought ... should it be y…
Comment: Help with species tree with orthofinder, iqtree and branch labeling by san96 ▴ 190
Thank you so much.
Comment: [vg giraffe] Unable to add read group to BAM file by saruman ▴ 10
Yes, it seems so. Thank you.
Comment: cellranger mkref fail/error by GenoMax 153k
> The thing is that I do not have a genome for these organisms. That is not what `cellranger mkref` is expecting. You could consider alt…
Comment: cellranger mkref fail/error by tatsispolychronis • 0
The thing is that I do not have a genome for these organisms. i made a transcriptome using TRinity and this is what I am feeding it. I do n…
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
Hi, I am not sure if i can call them good assemblies. Although based on QUAST and BUSCO stats, everything looks too good but somehow i hav…
Comment: cellranger mkref fail/error by GenoMax 153k
You need to provide the genome reference for the `--fasta` option as noted in https://www.10xgenomics.com/support/software/cell-ranger/late…
Answer: Methods to analyse structural similarity: co-evolution vs convergence by Joe 22k
Without historical data (ancient DNA) there's no way to ever really know this for certain. The best we can do is make inferences based on t…
Answer: vcf multisample by Pierre Lindenbaum 166k
eg : https://ega-archive.org/datasets/EGAD50000001683 > Merged VCF file from sporadic Meniere disease cohort (found using https://dat…
Comment: Genome Assembly QC from BAM files by GenoMax 153k
Since this saga has been on going for a long time, it will be helpful to add a comment as to how you finally got to this point of what seem…
Comment: Methods to analyse structural similarity: co-evolution vs convergence by dthorbur ★ 3.1k
A few comments. 1. Coevolution of a trait between 2 organisms can end up with a convergent structure with another organism. It's not e…
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
Thank you. Based on the description these two look really what i wanted to see.
Comment: miRNA low mapping ratings by i.sudbery 22k
Also, can you just clarify that the output above is from cutadapt or form miRDeep2?
Comment: miRNA low mapping ratings by i.sudbery 22k
What happens if you remove the `--minimum-length` requirement to cutadapt, and then run fastqc on the result - what size disitribution do y…
Answer: Genome Assembly QC from BAM files by colindaven 7.9k
You can have a look at the tools in the PAQman pipeline https://github.com/SAMtoBAM/PAQman, and maybe also Inspector https://github.com/Mag…
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