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121,921 results • Page 716 of 2439
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4
votes
2
replies
1.7k
views
What would be an error model for PacBio HiFi reads?
Assembly pacbio hifi
4.6 years ago by sebastian.schmidt.helsinki ▴ 10
0
votes
6
replies
1.1k
views
Estimate edit distance to a reference for a subset of bases in reads (bam files)
next-gen bam samtools sequence
updated 4.6 years ago by 166k • written 4.6 years ago by ▴ 30
4
votes
1
reply
1.7k
views
Tool: rBCS & pyBCS: open-source packages to support interactive visualizations of single-cell data
rna-seq single-cell scrna-seq
updated 2.3 years ago by 45k • written 4.6 years ago by ▴ 450
3
votes
2
replies
6.3k
views
error in density plot - methylation EPIC data
R bioconductor
updated 3.9 years ago by • 0 • written 6.5 years ago by ▴ 10
0
votes
0
replies
832
views
How to add coverage plots of 6 samples in Covid viral genome using circos like R packages
R genomic data visualization
4.6 years ago by S AR ▴ 80
1
vote
5
replies
3.6k
views
mummerplot results interpretation
mummer mummerplot alignment bash
4.6 years ago by langziv ▴ 70
1
vote
5
replies
1.5k
views
BCFTools query regex or boolean expression
bcftools
4.6 years ago by User000 ▴ 750
0
votes
2
replies
1.7k
views
How to do pca plot from .eigenvec files from Plink in R
R GWAs Plink
4.6 years ago by anithanagaraj93 ▴ 10
2
votes
2
replies
1.6k
views
Finding single-organism orthologs using NCBI Gene ID
RNA-Seq NCBI orthologs
updated 4.6 years ago by ▴ 60 • written 4.6 years ago by ▴ 90
2
votes
2
replies
1.7k
views
How to ignore "GT" from vcf file
bcftools nanopore medaka
updated 2.3 years ago by 45k • written 4.6 years ago by ▴ 80
6
votes
16
replies
9.2k
views
6 follow
Python script to remove sequences from a fasta file
Python fasta
updated 4.6 years ago by ▴ 80 • written 7.3 years ago by ▴ 50
16
votes
16
replies
5.9k
views
Species identifcation using 16s rRNA
16srRNA fasta
updated 2.0 years ago by 45k • written 4.6 years ago by ▴ 170
0
votes
4
replies
3.0k
views
Deseq2 : Script out of bounds
Genomics deseq2 R
updated 4.6 years ago by 20 • written 4.8 years ago by • 0
4
votes
4
replies
2.0k
views
Limma: how to get the overall logFC from a linear model without contrast?
limma metabolites metabolomics linear model
updated 4.6 years ago by 35k • written 4.6 years ago by ▴ 190
0
votes
1
reply
1.4k
views
Express v_1.5.1 Error: Transcript IDs from MultiFASTA do not match with (SAM/BAM) file.
rna-seq read counts
updated 4.6 years ago by 5.9k • written 4.7 years ago by ▴ 60
0
votes
3
replies
1.3k
views
which tool should be used to call the genotype?
ngs genotype gatk genotype calling variant
updated 4.6 years ago by 20 • written 4.7 years ago by • 0
1
vote
1
reply
1.1k
views
Extract CDS product from Genbank file with coordinate range
sequence genome gene
updated 4.6 years ago by ★ 3.9k • written 4.6 years ago by ▴ 10
0
votes
5
replies
1.3k
views
Optimized genome browser
RNA Genome
updated 4.6 years ago by 15k • written 4.6 years ago by ▴ 110
0
votes
0
replies
512
views
R, package: ldblock, function stack1kg error in opening BCFFile
SNP
4.6 years ago by ting835698 • 0
5
votes
11
replies
2.7k
views
Virsorter running error
next-gen sequencing
updated 4.6 years ago by ▴ 10 • written 5.6 years ago by ▴ 20
2
votes
2
replies
1.3k
views
Adjusting data for covariates
R
updated 2.5 years ago by 45k • written 4.6 years ago by ▴ 20
0
votes
9
replies
1.7k
views
fastqc report and quality check
RNA-seq
updated 2.1 years ago by 45k • written 4.6 years ago by • 0
0
votes
0
replies
920
views
get % of >= Q30 Bases (PF) per index with InterOp
next-gen
4.6 years ago by genya35 ▴ 50
0
votes
7
replies
5.0k
views
MUMmer plot visualization
MUMmer plot
updated 19 months ago by • 0 • written 4.6 years ago by ▴ 90
8
votes
4
replies
4.5k
views
Changing evalue doesn't change the results of blast
blast sequence alignment
updated 3.9 years ago by 45k • written 11.3 years ago by ▴ 290
2
votes
4
replies
835
views
Differences in results of Bowtie2
alignment
updated 4.6 years ago by 153k • written 4.6 years ago by ▴ 10
0
votes
0
replies
1.6k
views
Job: POSTDOC: Comparative genomics of bacterial pathogens (University of Pittsburgh)
postdoc
updated 2.5 years ago by 45k • written 4.6 years ago by ▴ 420
0
votes
0
replies
819
views
Error when running QoRTs for JunctionSeq
QoRTs JunctionSeq RNA-Seq
4.6 years ago by n.tear ▴ 80
3
votes
1
reply
870
views
Comparing expression of genes within an RNA-seq Experiment to confirm pluripotency
RNA-Seq
updated 3.6 years ago by 9.0k • written 4.6 years ago by ▴ 80
1
vote
3
replies
1.7k
views
How to run nucmer without reference? (viruses metagenomics)
assembly clustering metagenomics virus nucmer
updated 4.6 years ago by 7.9k • written 4.6 years ago by ▴ 160
1
vote
2
replies
1.8k
views
Recommend me R packages for text mining PubMed abstracts
R text mining
updated 4.6 years ago by 27k • written 4.6 years ago by ▴ 20
3
votes
7
replies
2.8k
views
Trying to refine REST API query
R ensembl API
updated 4.6 years ago by 24k • written 4.6 years ago by • 0
1
vote
4
replies
1.7k
views
Checking ReadGroup name in BAM file error: E26: Hebrew cannot be used: Not enabled at compile time
RNA-Seq GATK
updated 4.6 years ago by 166k • written 4.6 years ago by ▴ 20
0
votes
0
replies
877
views
FigTree Error: File contains no tree
software error alignment
4.6 years ago by philipp.baumann125 • 0
0
votes
0
replies
895
views
MUMmer for structural variant call
MUMmer structural variants circlator
4.6 years ago by rthapa ▴ 90
0
votes
1
reply
911
views
Problem using CNVkit with RNA-Seq Data to call CNV with Ensembl GRCh37 v75 annotation file
RNA-Seq CNV CNVkit
4.6 years ago by lumal29 ▴ 80
0
votes
2
replies
6.0k
views
PEPATAC error: ConnectionResetError: [Errno 104] Connection reset by peer
ATAC-seq PEPATAC refgenie
updated 4.6 years ago by • 0 • written 4.7 years ago by ▴ 50
2
votes
5
replies
1.3k
views
Forum: Unit test / integration test packages for R for bioinformatic projects?
R
updated 2.5 years ago by 45k • written 4.6 years ago by ★ 3.5k
0
votes
0
replies
750
views
What is the cut off used in TCGA vcf files for allelic frequency for calling it as somatic?
tcga vcf
4.6 years ago by DareDevil ★ 4.4k
0
votes
0
replies
454
views
Filtering of Predicted Transcripts
RNA-Seq assembly rna-seq
4.6 years ago by cc_prolix • 0
1
vote
2
replies
803
views
filter varaints from vcf sample based on their presence in N number of samples ?
vcf SNP alignment
updated 4.6 years ago by 166k • written 4.6 years ago by ▴ 350
1
vote
8
replies
1.8k
views
PCA - untreated sample cluster separated
R bulk-RNAseq PCA variability
4.6 years ago by camillab. ▴ 160
0
votes
2
replies
3.4k
views
Seurat VlnPlot vs PercentageFeatureSet expression level
R RNA-Seq
4.6 years ago by Jeffrey3555054 ▴ 20
6
votes
7
replies
8.7k
views
grep things and counting line number in R
R
updated 4.6 years ago by 20 • written 7.4 years ago by ▴ 140
7
votes
4
replies
2.2k
views
getBM results are not in the same order as the input in the "values" argument
GEO biomaRt
updated 4.6 years ago by 89k • written 4.6 years ago by ▴ 50
0
votes
6
replies
3.0k
views
bedtools genome file
sequencing bedtools
4.6 years ago by tom • 0
0
votes
0
replies
751
views
Using different tools for different database sequences to identify antibiotic resistance genes.
NGS alignment metagenomics antibiotic resistance
4.6 years ago by dymphan.17phd ▴ 10
6
votes
2
replies
2.1k
views
Find structural variants comparing two assemblies
Assembly genome comparative genomics
updated 4.6 years ago by ▴ 20 • written 6.1 years ago by ▴ 80
6
votes
4
replies
5.1k
views
Are there any tutorials available for Nanostring data differential expression analysis using DEseq2 ?
nanostring deseq2 limma
updated 2.5 years ago by 45k • written 4.6 years ago by ★ 4.4k
0
votes
1
reply
1.5k
views
Making PLINK compatible files from VCF file without phenotype information
plink gwas vcf
4.6 years ago by mfshiller ▴ 20
121,921 results • Page 716 of 2439
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A: Binning Over Genes And Calculating The Coverage [Bedops/Bedmap]
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Recent Replies
Comment: SNP calling with bacterial assembled genome by GenoMax 153k
> Is it possible to do this at the assembly level? By aligning to a reference you can find the differences between your assembly and the …
Comment: miRNA low mapping ratings by i.sudbery 22k
4bp would suggest there was nothing cloned into the library. But i'm a bit confused. In example in the question, it talks about 50,000 re…
Comment: miRNA low mapping ratings by GenoMax 153k
> while fewer than 100,000 reads were around 18-22 bp. That is why are you likely seeing the numbers you are observing in alignments. Wa…
Comment: Help with Model by Joe 22k
I would imagine this is something one of the AI code tools could handle.
Comment: cellranger mkref fail/error by ATpoint 89k
I think OCM = https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-3p-what-is-cellplex#on-chip Seconding to…
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…
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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…
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