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121,919 results • Page 712 of 2439
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3
votes
6
replies
3.4k
views
User-defined coverage in CollectHsMetrics [Picard]
next-gen picard coverage broadinstitute
updated 4.6 years ago by • 0 • written 8.2 years ago by ▴ 190
3
votes
14
replies
3.7k
views
Samtools depth to get the read depth
sequencing RNA-Seq
4.6 years ago by bandanaschapagain ▴ 40
4
votes
4
replies
7.2k
views
How to get real cell names from Seurat Object?
rna-seq
updated 4.6 years ago by ▴ 250 • written 4.6 years ago by ▴ 150
0
votes
0
replies
777
views
Is there a way to identify which MSTRGs (novel StringTie transcripts) are potential novel ncRNAs?
MSTRG RNAseq StringTIe ncRNA Novel Transcripts
4.6 years ago by Jen ▴ 100
7
votes
23
replies
8.1k
views
Batch download genome feature file by RefSeq
gbff ncbi refseq
4.6 years ago by ben83 ▴ 50
3
votes
3
replies
4.6k
views
How to download a list of all KEGG orthologs with respect to KEGG module (or pathway) in Python?
kegg database python
updated 3.2 years ago by • 0 • written 4.6 years ago by ▴ 750
3
votes
2
replies
1.8k
views
How to check for completeness of a mitochondrial or chloroplast genome?
genome-completeness organelles
updated 24 months ago by 45k • written 4.6 years ago by ▴ 170
0
votes
2
replies
1.9k
views
minimap2 alignment for maker
maker minimap2 annotation alignment
4.6 years ago by gilsorek12 ▴ 10
0
votes
0
replies
673
views
How can I analyze a VCF dataset without an annotated reference genome
RNA-Seq R genome gatk galaxy
4.6 years ago by julianneradford ▴ 20
2
votes
6
replies
4.8k
views
convert DNA FASTA file to RNA FASTA file
RNA-Seq ChIP-Seq sequence
updated 4.6 years ago by 13k • written 4.6 years ago by ▴ 140
0
votes
0
replies
588
views
Centrifuge (Classifier for metagenomic sequences)
software error
4.6 years ago by amanpruthi15 • 0
0
votes
3
replies
2.1k
views
How can I run "gene set enrichment" (not necessarily GSEA) with only one condition?
metagenomics gene set enrichment analysis GSEA
4.6 years ago by O.rka ▴ 750
0
votes
0
replies
635
views
smallRNA-seq alignment with bowtie1:what is the argument for handling multi-mapped reads?
alignment smallRNA-seq bowtie1 multi-mapped reads
updated 4.6 years ago by 153k • written 4.6 years ago by • 0
1
vote
1
reply
1.6k
views
tsv file genome coverage
tsv genome
updated 4.6 years ago by 20 • written 4.6 years ago by ▴ 50
0
votes
8
replies
1.9k
views
Finding suboptimal alignments
sequencing DNA alignment
updated 4.6 years ago by ★ 30k • written 4.6 years ago by ▴ 10
13
votes
11
replies
6.1k
views
8 follow
Visualization of protein structure in R (Shiny)
R rshiny pdb protein structure visualization
updated 4.5 years ago by ▴ 90 • written 5.0 years ago by ▴ 40
0
votes
1
reply
2.2k
views
Convert .sqn file to .gbk
organelle
updated 24 months ago by 45k • written 4.6 years ago by ▴ 170
1
vote
3
replies
2.5k
views
PCA with PLINK and SmartPCA: same imput file but different results in my plot. Why?
PCA PLINK smartPCA EIGENSTRAT plot
4.6 years ago by francesca94.minnai • 0
3
votes
1
reply
1.7k
views
Tool for extracting copy number alterations from a .maf mutation file
cna maf
updated 4.6 years ago by 89k • written 4.6 years ago by ▴ 90
1
vote
4
replies
1.6k
views
Change sample order in plotHeatmap?
deepTools plotHeatmap computeMatrix
updated 3.1 years ago by • 0 • written 4.6 years ago by • 0
3
votes
5
replies
3.0k
views
Clustering sequences with low identity
clustering sequences
updated 4.6 years ago by ★ 30k • written 4.6 years ago by ▴ 870
0
votes
1
reply
742
views
ICGC data download
ICGC local server
4.6 years ago by Zahra ▴ 110
0
votes
1
reply
784
views
how to make BBmerge produce same strand fastq file
BBmerge
4.6 years ago by shangguandong1996 ▴ 30
3
votes
5
replies
2.1k
views
Newbie CIGAR question
SNP alignment sequence
updated 4.6 years ago by 20 • written 8.9 years ago by • 0
1
vote
0
replies
1.4k
views
How to get RSIDs of indels from GWAS summary statistics
R gene snp
4.6 years ago by Fede_Santos95 ▴ 20
2
votes
2
replies
943
views
VCF keep only genotyped positions
vcf genotype snp
4.6 years ago by sahahig469 ▴ 10
0
votes
2
replies
894
views
compare a list of RNA with RNA sequence in RFAM using python
RNA-Seq RFam Python
4.6 years ago by phangou10 • 0
0
votes
0
replies
586
views
Duplicates probability depending on the number of flow cells
next-gen sequencing duplicates
4.6 years ago by kseniya.petrova • 0
0
votes
7
replies
1.6k
views
deseq2 design with two variables
deseq2 design
4.6 years ago by biosjm • 0
2
votes
1
reply
996
views
Is OMA suitable for prediction of GO function in metagenomic datasets?
OMA GO_Label
updated 4.6 years ago by ▴ 60 • written 4.8 years ago by ▴ 10
0
votes
4
replies
1.4k
views
Oligo algorithm analyzer
oligo analyzer primer
4.6 years ago by anasofiamoreira94 ▴ 80
2
votes
3
replies
1.3k
views
How to convert gff3 format, PASApipeline
RNA-Seq Assembly
updated 4.6 years ago by 9.3k • written 4.6 years ago by • 0
1
vote
11
replies
2.2k
views
ground truth dataset for BAM read counts
genome alignment read counts ground truth
4.6 years ago by Marius ▴ 30
1
vote
1
reply
1.0k
views
Splice junction coordinates for Ensembl transcripts
Ensembl Splicing Annotation
updated 4.6 years ago by 24k • written 4.6 years ago by • 0
8
votes
3
replies
1.5k
views
how to select features for high dimension data?
machine-learning
updated 22 months ago by 45k • written 4.6 years ago by ▴ 70
16
votes
10
replies
8.2k
views
from txt to bed
ChIP-Seq
updated 4.6 years ago by 20 • written 8.5 years ago by ▴ 210
0
votes
0
replies
396
views
Mitochondrial genome sequence
sequencing
4.6 years ago by ganesh_swamy2005 • 0
3
votes
9
replies
3.7k
views
Ubuntu 20.04.1 for genomic data analysis
next-gen sequencing genome
updated 4.6 years ago by ▴ 940 • written 4.6 years ago by • 0
1
vote
0
replies
1.1k
views
Job: Postdoctoral fellow -- genetic/molecular epidemiology
multiomics data-analysis
updated 2.3 years ago by 45k • written 4.6 years ago by ▴ 10
3
votes
5
replies
4.2k
views
Post-imputation QC GWAS analysis
GWAS Rstudio Imputation TopMed
updated 4.6 years ago by 20 • written 5.1 years ago by • 0
0
votes
1
reply
1.2k
views
Trimming Illumina Seq with TRIMMOMATIC
trimmomatic GBS Illumina
4.6 years ago by giulia.trauzzi ▴ 30
0
votes
2
replies
1.2k
views
bedtools genomecov max function not working correctly
Assembly bedtools genomecov
updated 2.3 years ago by 45k • written 4.6 years ago by ▴ 10
4
votes
2
replies
6.4k
views
problems installing HTSeq
RNA-Seq HTSeq DEXSeq
updated 4.6 years ago by 20 • written 8.4 years ago by ★ 1.3k
1
vote
2
replies
1.7k
views
GSEA with GGProfiler2 (?"annotated" vs "known" for background control)
RNA-Seq GSEA GGProfiler2
updated 4.6 years ago by 89k • written 4.6 years ago by • 0
0
votes
0
replies
642
views
database about population data of aquatic animal organisms
databases
4.6 years ago by eridanus ▴ 40
0
votes
0
replies
653
views
Can I do microarray meta-analysis combinning Induced pluripotent stem cells and neurons?
R geno
4.6 years ago by firstorthopedicdoctor ▴ 30
2
votes
2
replies
1.9k
views
Merging PacBio and Nanopore reads
Nanopore Pacbio next-gen long reads Assembly
updated 4.6 years ago by ▴ 130 • written 4.6 years ago by ▴ 10
2
votes
7
replies
3.9k
views
Finding assembled transcript sequences from StringTie output
RNA-Seq StringTie Assembled Transcripts Sequences
4.6 years ago by Jen ▴ 100
2
votes
3
replies
861
views
ENCODE terminology question
sequencing alignment
updated 4.6 years ago by 22k • written 4.6 years ago by ▴ 30
0
votes
5
replies
1.8k
views
MEgene correlated to triat and Gene signficance coorelated to triat
WGCNA andres.firrincieli
updated 4.4 years ago by ▴ 40 • written 4.6 years ago by ▴ 130
121,919 results • Page 712 of 2439
Recent Votes
A: read.table does not read in all rows!
A: read.table does not read in all rows!
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
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Recent Replies
Comment: miRNA low mapping ratings by Ant ▴ 50
The first one it's the results from Cutadapter and the second block from miRDeep2.
Comment: miRNA low mapping ratings by Ant ▴ 50
Thanks for the reply, when running: cutadapt -a AACTGTAGGCACCATCAAT -M 30 -o example_trimmed.fastq.gz data/xxx.fastq.gz, the sequence le…
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?
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