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0
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117
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Best codeml model for estimating omega, M0 ?
codeml ete3 evol
29 days ago by Adrian Pelin ★ 2.6k
0
votes
1
reply
341
views
PAML/codeml Poxvirus dN/dS
dNdS codeml selection
updated 7 months ago by ▴ 490 • written 7 months ago by ★ 2.6k
2
votes
2
replies
536
views
Estimating mRNA 5' degradation from RNA-seq illumina strand-specific reads
mRNA decay RNA-seq
17 months ago by Adrian Pelin ★ 2.6k
3
votes
1
reply
487
views
Differential pathways between 2 gene sets
enrichment GO KEGG
updated 18 months ago by 13k • written 18 months ago by ★ 2.6k
2
votes
4
replies
2.6k
views
List of human protein coding genes with given name (known function?)
RNA-Seq Annotation Human
updated 2.6 years ago by ★ 9.4k • written 4.7 years ago by ★ 2.6k
0
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6
replies
984
views
Need opinion on correct bioinfo analysis; NGS on virus competition exp
Abundace RNA-Seq
4.0 years ago by Adrian Pelin ★ 2.6k
0
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6
replies
4.5k
views
Blast2Go Local Www-Blast Not Working
updated 4.1 years ago by 20 • written 10.4 years ago by ★ 2.6k
2
votes
3
replies
1.5k
views
Advice on DE analysis of mouse and human merged RNA-seq data
RNA-Seq DEseq Human Mouse
updated 4.5 years ago by 14k • written 4.6 years ago by ★ 2.6k
1
vote
11
replies
4.1k
views
bedtools merge - removing features completly overlapped by other features
bedtools
updated 4.6 years ago by ▴ 40 • written 6.6 years ago by ★ 2.6k
10
votes
3
replies
2.0k
views
Crazy high file size for human genome from Ensembl
Ensembl
updated 4.6 years ago by 23k • written 4.6 years ago by ★ 2.6k
4
votes
7
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1.6k
views
Extracting reads mapping to CDS regions but not the first 45bp after ATG
RNA-Seq bed bam
updated 4.7 years ago by 161k • written 4.7 years ago by ★ 2.6k
0
votes
0
replies
759
views
Mapping short 26-32nt RPF reads to human genome
RNA-Seq Ribosomal profiling Mapping RPF
4.7 years ago by Adrian Pelin ★ 2.6k
3
votes
9
replies
2.0k
views
From per bp coverage to average coverage in 10bp intervals
genome DNA-seq bam
updated 4.7 years ago by 35k • written 4.7 years ago by ★ 2.6k
0
votes
5
replies
1.7k
views
HISAT2/stringtie: intron impact on expression
HISAT2 stringtie TPM RNA-seq mRNA Expression
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ★ 2.6k
3
votes
2
replies
801
views
Generating Interaction map
cytoscape interactome R
updated 4.9 years ago by 27k • written 4.9 years ago by ★ 2.6k
4
votes
5
replies
4.2k
views
Perl Script To Retrieve All Orf?
orf perl
updated 5.0 years ago by ▴ 20 • written 10.1 years ago by ★ 2.6k
12
votes
6
replies
11k
views
HISAT2 output direct to bam
RNA-Seq samtools
updated 2.7 years ago by 82k • written 5.0 years ago by ★ 2.6k
1
vote
2
replies
1.7k
views
Extracting sequence and annotation of a particular gene
Annotation GTF
updated 5.1 years ago by 82k • written 5.1 years ago by ★ 2.6k
2
votes
2
replies
1.1k
views
Comparing NCI-60 transcriptome with another variable to determine genes that correlate
RNA-Seq NCI60
updated 5.4 years ago by ▴ 350 • written 5.4 years ago by ★ 2.6k
2
votes
4
replies
2.3k
views
bash & quickGO to download gene symbols of a GO term
Annotations GO bash
updated 5.4 years ago by 7.5k • written 5.4 years ago by ★ 2.6k
6
votes
7
replies
2.1k
views
RNA-seq analysis of virally infected cells
RNA-Seq virus host
updated 5.5 years ago by 20 • written 5.7 years ago by ★ 2.6k
6
votes
7
replies
4.6k
views
How To Check For Ploidy Using Ngs Only?
ngs mapping
updated 5.6 years ago by ▴ 220 • written 10.2 years ago by ★ 2.6k
2
votes
8
replies
4.0k
views
Demultiplexing SRA data
SRA NGS Illumina multiplex
updated 5.6 years ago by 43k • written 8.2 years ago by ★ 2.6k
11
votes
8
replies
6.8k
views
Annotating/Finding "NNNNNN" scaffold gaps in genome assembly
bed NGS scaffolding Assembly
updated 18 months ago by 43k • written 8.7 years ago by ★ 2.6k
4
votes
8
replies
3.1k
views
How To Phase Haplotypes In A Highly Polymorphic Genome
vcf variant-calling
updated 6.2 years ago by 20 • written 10.3 years ago by ★ 2.6k
3
votes
5
replies
2.0k
views
Detecting junctions from reads spanning large indels
DNA-seq sam
updated 6.5 years ago by 161k • written 6.5 years ago by ★ 2.6k
1
vote
4
replies
4.2k
views
Phylogeny: tree branch length on a log scale
FigTree phylogeny
6.7 years ago by Adrian Pelin ★ 2.6k
4
votes
2
replies
5.3k
views
Command blast excluding species
blast
updated 6.8 years ago by 20 • written 9.9 years ago by ★ 2.6k
2
votes
4
replies
3.5k
views
Detecting Variants near repeats
freebayes vcf bam repeats
updated 7.1 years ago by ★ 3.6k • written 9.9 years ago by ★ 2.6k
15
votes
7
replies
14k
views
6 follow
Removing PCR duplicates from .fastq without .bam alignment
PCR duplicates illumina fastq
updated 2.2 years ago by 43k • written 9.4 years ago by ★ 2.6k
1
vote
3
replies
1.3k
views
Merge/Collapse regions within a certain distance
bedtools
updated 7.3 years ago by 161k • written 7.3 years ago by ★ 2.6k
1
vote
1
reply
1.5k
views
multiIntersectBed for SNPs, need to compare but not merge intervals
SNP bedtools intersect
updated 7.3 years ago by 35k • written 7.3 years ago by ★ 2.6k
2
votes
4
replies
3.8k
views
Genetic Distance Versus Physical Distance
distance
updated 7.4 years ago by ▴ 10 • written 10.3 years ago by ★ 2.6k
6
votes
4
replies
2.4k
views
Predict AA sequence from assembled transcripts
RNA-Seq Assembly nt2aa
updated 23 months ago by 43k • written 9.2 years ago by ★ 2.6k
6
votes
6
replies
6.4k
views
Fisher's exact test gives p-value 0
enrichment R fisher's exact test
7.9 years ago by Adrian Pelin ★ 2.6k
2
votes
3
replies
7.5k
views
RPS Blast, COG and KOG analysis
KOG COG RPSBLAST
updated 8.0 years ago by ▴ 150 • written 9.1 years ago by ★ 2.6k
3
votes
4
replies
5.5k
views
BaseSpace says NextSeq run finished, can't download FastQ
DNA-Seq illumina basespace
updated 8.0 years ago by 13k • written 8.0 years ago by ★ 2.6k
2
votes
4
replies
2.6k
views
RNA-seq experiment of mouse organs
RNA-Seq mouse SRA NGS
updated 8.2 years ago by 35k • written 8.2 years ago by ★ 2.6k
16
votes
7
replies
9.4k
views
7 follow
Any software to view newick/nexus trees command line?
phylogeny cmd
updated 2.1 years ago by 43k • written 9.4 years ago by ★ 2.6k
2
votes
1
reply
1.7k
views
Find restriction enzyme combo that cuts every 2-3kb best
Genome restriction
updated 21 months ago by 43k • written 8.4 years ago by ★ 2.6k
0
votes
0
replies
2.4k
views
UCSC_TFBS enrichment with DAVID
TF DAVID
8.4 years ago by Adrian Pelin ★ 2.6k
0
votes
2
replies
2.2k
views
Determine likely TF(s) regulating a list of genes
microarray gene regulatiom ncRNA TF
updated 8.4 years ago by ★ 1.4k • written 8.4 years ago by ★ 2.6k
4
votes
15
replies
7.1k
views
8 follow
Error in SNP calling, samtools
NGS bcftools vcf SNP
updated 2.5 years ago by 43k • written 9.8 years ago by ★ 2.6k
4
votes
5
replies
2.9k
views
bwa mapping to several similar strains, restrict maximum hits?
bwa sam bwa-mem bwa-aln fasta
updated 2.2 years ago by 43k • written 9.5 years ago by ★ 2.6k
1
vote
2
replies
2.3k
views
Strategy to get rid of fake mate pairs
NGS mate-pair denovo Assembly genome
8.5 years ago by Adrian Pelin ★ 2.6k
1
vote
11
replies
3.8k
views
Calling large indels from NGS
NGS large-indels samtools
updated 20 months ago by 43k • written 8.5 years ago by ★ 2.6k
1
vote
2
replies
2.0k
views
MDS plot for miRNA data
RNA-Seq smallRNA MDS
8.6 years ago by Adrian Pelin ★ 2.6k
0
votes
0
replies
1.7k
views
Running LG+I+G in phylobayes
phylogenetics phylobayes alignment
updated 19 months ago by 43k • written 8.6 years ago by ★ 2.6k
1
vote
3
replies
5.6k
views
Plotting sequence similarity/identity of a multiple sequence alignment
MSA R plotting
updated 8.8 years ago by 141k • written 8.8 years ago by ★ 2.6k
0
votes
0
replies
2.3k
views
DNASP analysis of recombination, is my analysis meaningful?
DNASP recombination Rm
updated 8.9 years ago by 20 • written 9.1 years ago by ★ 2.6k
111 results • Page 1 of 3
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