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1,000 results • Page 3 of 20
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4
votes
4
replies
359
views
Average expression of a sample in single-cell data
single-cell rna-seq
23 days ago by newuser2024 • 0
4
votes
12
replies
7.8k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 11 weeks ago by ▴ 10 • written 3.4 years ago by ▴ 60
4
votes
9
replies
1.2k
views
Snakemake issue with wrappers
Python Snakemake
5 months ago by Begonia_pavonina ▴ 150
4
votes
3
replies
303
views
Should you remove PCR duplicates for kmer counting?
kmer dedup duplicates
updated 11 weeks ago by 4.6k • written 11 weeks ago by ▴ 30
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 17 days ago by 43k • written 3.7 years ago by ▴ 20
4
votes
3
replies
686
views
How to interpret output of PLINK association test (--assoc)
assoc
updated 8 months ago by 11k • written 8 months ago by ▴ 10
4
votes
1
reply
623
views
How to interpret Clustree results?
scRNA clustering clustree
updated 8 months ago by 3.9k • written 8 months ago by ▴ 120
4
votes
3
replies
587
views
Over Representation analysis altered pathways in common between comparisons plot
R Visualization DGE ORA
updated 6 months ago by ★ 2.0k • written 6 months ago by ▴ 10
4
votes
3
replies
745
views
BBduk log and stats appear to be inconsistent
bbduk bbmap
updated 11 months ago by 141k • written 11 months ago by ★ 1.7k
4
votes
4
replies
602
views
Request for a linkage analysis tutorial
linkage
updated 8 months ago by 141k • written 8 months ago by ★ 2.9k
4
votes
13
replies
864
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 8 days ago by ★ 1.7k • written 14 days ago by • 0
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter genome
updated 10 months ago by 43k • written 4.6 years ago by ▴ 120
4
votes
11
replies
1.8k
views
PCA WITH PLINK
PLINK
updated 8 months ago by 87k • written 8 months ago by • 0
4
votes
4
replies
479
views
Correlation for ATAC-Seq and Chip-Seq
RNA-Seq Chip-Seq ATAC-Seq
8 weeks ago by qudrat.nii ▴ 10
4
votes
6
replies
955
views
Open-Source software. Good or bad for the market?
genomic-analysis software
updated 11 months ago by 43k • written 6.2 years ago by • 0
4
votes
6
replies
2.1k
views
Single nucleotide Polymorphism (SNP)
SNP
updated 10 months ago by 43k • written 9.0 years ago by ▴ 10
4
votes
6
replies
2.4k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 10 months ago by • 0 • written 20 months ago by ▴ 20
4
votes
6
replies
337
views
Protein loops
protein Loop
6 weeks ago by Curious ▴ 10
4
votes
7
replies
1.0k
views
Statistical test to compare data across timepoints
Statistics
updated 6 months ago by 4.5k • written 6 months ago by ▴ 20
4
votes
6
replies
2.6k
views
Convert Nanopore Fast5 files to Fasta format
fast5 fasta Nanopore
11 months ago by Sowmya Pulapet ▴ 70
4
votes
6
replies
1.0k
views
Python script to automatically read in, name output files & parse R1 & R2 fastq.gz files when given an input directory with raw data files
python fastq
9 months ago by eorr ▴ 30
4
votes
4
replies
845
views
retaining only the clusters of interest
seurat single-cell scRna-seq
updated 10 months ago by 43k • written 10 months ago by • 0
4
votes
4
replies
3.3k
views
Unable to install Autogrid4
autogrid software-error autogrid4
updated 11 months ago by 43k • written 3.1 years ago by • 0
4
votes
11
replies
630
views
Remove X in row name with only number
GSVA
updated 11 weeks ago by 43k • written 11 weeks ago by ▴ 260
4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan SNP
updated 10 months ago by 43k • written 9.5 years ago by • 0
4
votes
3
replies
483
views
Parsing columns with awk
awk
updated 5 months ago by 43k • written 5 months ago by ▴ 300
4
votes
5
replies
1.2k
views
tranfering sam file easy and fast way
SAM RNA-seq hisat2
updated 8 months ago by 43k • written 2.3 years ago by • 0
4
votes
5
replies
382
views
Filter out miRNA from ncRNA dataset
bowtie bowtie2 miRNA filtering ncRNA
updated 9 weeks ago by 82k • written 9 weeks ago by ▴ 10
4
votes
16
replies
955
views
hisat2 location does not exist
hisat2
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
4
votes
8
replies
1.2k
views
Error executing nf-core/metaboigniter pipeline
nf-core metaboigniter nextflow
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
4
votes
9
replies
568
views
variant calling
variant-calling
updated 22 days ago by 43k • written 23 days ago by • 0
4
votes
5
replies
2.0k
views
Whole blood single cell RNA-seq dataset?
RNA-Seq scRNA-Seq whole blood single cell
12 months ago by predeus ★ 1.9k
4
votes
7
replies
544
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 11 days ago by 43k • written 13 days ago by ▴ 20
4
votes
2
replies
555
views
Can I still remove ambient RNA if I do not have raw barcode-gene matrix?
SoupX
6 months ago by malonzm1 ▴ 20
4
votes
7
replies
1.4k
views
.bed files from sequencing platform not containing intervals of "alt", "random" haplotypes. How do I perform coverage and haplotype caller?
exome .bed haplotypes HG38 coverage
updated 9 months ago by 141k • written 9 months ago by • 0
4
votes
16
replies
1.7k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools RNAseq samtools BAM
updated 9 weeks ago by 43k • written 7 months ago by • 0
4
votes
2
replies
2.2k
views
Bfast Match Paired End Reads - Reports Half Total Number Of Reads
paired-end alignment next-gen
updated 10 months ago by 43k • written 11.3 years ago by ▴ 50
4
votes
4
replies
602
views
I cannot install anaconda on ubuntu 22.04
ubuntu anaconda Conda
updated 8 months ago by 43k • written 8 months ago by ▴ 10
4
votes
3
replies
1.0k
views
What is the difference between vst and rlog to perform PCA ?
rlog PCA vsd
updated 11 months ago by 82k • written 11 months ago by ▴ 160
4
votes
6
replies
801
views
how to plot SV(structural variants) from many assemblies of a given locus
SV
11 months ago by natalev ▴ 20
4
votes
14
replies
2.6k
views
Is it possible to annotate single genes by snpeff
snp vcf
updated 10 months ago by 43k • written 6.7 years ago by ▴ 70
4
votes
14
replies
1.1k
views
remove white space in fastq file
fastq
updated 4 months ago by 141k • written 4 months ago by • 0
4
votes
5
replies
533
views
Which refseq_protein db to choose for zingiberaceae
local blastp blast
updated 8 months ago by 141k • written 8 months ago by • 0
4
votes
8
replies
1.9k
views
Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE …
super-enhancers Enhancers
updated 12 weeks ago by ★ 16k • written 3 months ago by • 0
4
votes
6
replies
1.2k
views
Transcript quantification
rna-seq transcriptome SRA
updated 10 months ago by 82k • written 10 months ago by • 0
4
votes
6
replies
1.8k
views
Failure in installing the ggtree, enrichplot, and ggtree (Bioconductor packages )
Bioconductor
updated 9 months ago by 141k • written 9 months ago by • 0
4
votes
7
replies
763
views
Alternative for grep in a for loop
linux
updated 6 months ago by 43k • written 6 months ago by ▴ 20
4
votes
6
replies
932
views
How to pass from DNA to AA fasta
genetics
updated 11 months ago by ★ 2.4k • written 11 months ago by • 0
4
votes
5
replies
2.4k
views
Merge CNVnator output of multiple samples
CNV WGS
updated 10 months ago by 43k • written 6.7 years ago by ▴ 40
4
votes
7
replies
810
views
SNP IDs
SNP
5 months ago by kl ▴ 10
1,000 results • Page 3 of 20
Recent Votes
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
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Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package by DKA ▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis by ATpoint 82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets by ATpoint 82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files by QX • 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis by kilcdincer ▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases by GenoMax 141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases by 5heikki 11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work? by Bioinfotec ▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes by Bioinfotec ▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question by Bioinfotec ▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification by GenoMax 141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing by rohitsatyam102 ▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification by ATpoint 82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
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