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121,913 results • Page 701 of 2439
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2
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1.5k
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plotCorrelation scatter plot ChIP-seq data
ChIP-Seq deepTools correlation
4.5 years ago by Marco Pannone ▴ 810
1
vote
1
reply
2.4k
views
PRSice on Imputation vcf.gz data; conversion of files
prisce imputation vcf plink bgen
updated 4.5 years ago by ★ 4.8k • written 4.5 years ago by • 0
0
votes
0
replies
592
views
sample size on Pearson's correlation
wgcna scale-free-topology coexpression Network
4.5 years ago by hubsnets ▴ 30
3
votes
4
replies
2.0k
views
Demultiplexing of Smart-Seq2 library using bcl2fastq
bcl2fastq smart-seq2 sequencing
4.5 years ago by gnomee ▴ 50
1
vote
3
replies
1.0k
views
How do you design primers with sequencing adapters to amplify CRISPR-edited regions?
primer-design crispr primer3
updated 4.5 years ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
3
replies
2.4k
views
How can I make parsing big fasta with biopython SeqIO go faster?
fasta biopython seqio extract python
updated 4.5 years ago by 22k • written 4.5 years ago by ▴ 40
5
votes
3
replies
16k
views
The fonts and size of a tree displayed by ggtree
R
updated 4.5 years ago by ▴ 30 • written 7.4 years ago by ▴ 110
0
votes
2
replies
1.8k
views
read10X ERROR Seurat
read10x singlecell rna R seurat
updated 4.5 years ago by 13k • written 4.5 years ago by ▴ 20
0
votes
2
replies
1.2k
views
Annotation of results from CD-HIT web server
CD-HIT
updated 4.5 years ago by ★ 30k • written 4.5 years ago by • 0
0
votes
0
replies
697
views
What is the common lncRNA-target reference file with proper lncRNA gene name?
lncRNA gene sequencing genome sequence
4.5 years ago by Apex92 ▴ 320
2
votes
2
replies
1.8k
views
How to get `assembly-stats` command?
ubuntu stats assembly-stats assembly sequencing
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 20
1
vote
1
reply
541
views
some question about the NGS sequence
rna-seq
4.5 years ago by 972050141 • 0
0
votes
0
replies
578
views
Bulk download from CNGBdb?
cngb Assembly genome
4.5 years ago by matthewcrossie • 0
0
votes
1
reply
788
views
To retrive all sequences
Assembly
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
0
votes
2
replies
1.1k
views
Modifying an annotation files after transgene insertion
transgene insertion gtf annotation
4.5 years ago by Assa Yeroslaviz ★ 1.9k
1
vote
3
replies
1.2k
views
how to annotate Circular RNA gene type?
RNA-Seq Circular RNA annotation
4.5 years ago by modarzi ▴ 170
3
votes
6
replies
2.8k
views
Covariate correction which data take for downstream analysis?
R linear-regression residual fitted-values
updated 3.9 years ago by ▴ 220 • written 4.5 years ago by ▴ 160
0
votes
0
replies
1.6k
views
Getting KOBAS species annotation database for salmon (salmo salar)
KOBAS kegg enrichment analysis
4.5 years ago by Michael 56k
0
votes
0
replies
702
views
Advice setting up harware/software for snRNA-seq analysis for a newbie
hardware software single-cell
4.5 years ago by georgytos95 • 0
0
votes
3
replies
2.3k
views
Getting Uniprot accession number
gene RNA-Seq
updated 4.5 years ago by ★ 2.4k • written 4.8 years ago by ▴ 50
1
vote
0
replies
700
views
What is the best approach to correlate expression levels, mutated genes and clinical variables
RNA-Seq correlation mutation
4.5 years ago by Lila M ★ 1.3k
3
votes
6
replies
2.8k
views
low assignment reads % in RNA-seq
rna-seq R
4.5 years ago by parinv ▴ 80
0
votes
0
replies
641
views
Why could I be having only NAs for p_val and p_val_adj in Seurat DGE analysis?
RNA-Seq R rna-seq next-gen gene
4.5 years ago by charlesgwellem ▴ 10
0
votes
4
replies
2.1k
views
Non-linear relationship between a cell's mitochondrial content and detection of ribosomal genes ssen in single cell rNA seq
RNA-Seq next-gen
updated 4.5 years ago by ▴ 180 • written 4.6 years ago by ▴ 10
1
vote
0
replies
751
views
Forum: Determining Heteroplasmy per sample
heteroplasmy bcftools
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 10
2
votes
3
replies
1.2k
views
Chip-seq balcklisted region information for the latest version of genome ensembl GRCm38
ChIP-Seq alignment
4.5 years ago by luckysardar171 ▴ 20
0
votes
1
reply
830
views
How can I detect small deletion
SNP indel GATAk
4.5 years ago by dyfn1947 • 0
2
votes
4
replies
2.6k
views
HTSeq counts gives zero when I can see the reads in the BAM file
htseq htseq-counts
4.5 years ago by blur ▴ 280
0
votes
1
reply
2.2k
views
Blastn: In The Scoring Parameters, What Does "Linear" Mean?
blastn alignment
updated 4.5 years ago by 20 • written 11.5 years ago by ▴ 180
0
votes
0
replies
1.2k
views
converting bedgraph to Bigwig by HOMER
bedGraph ChIP-seq BigWig HOMER
updated 2.5 years ago by 45k • written 4.5 years ago by • 0
3
votes
4
replies
4.1k
views
GEOquery loading error.
r geo
updated 4.5 years ago by ▴ 270 • written 4.6 years ago by ▴ 10
0
votes
2
replies
919
views
Violation of Independence test for differential methylation (DM)
methylation differential methylation
4.5 years ago by CY ▴ 750
0
votes
3
replies
1.4k
views
GO annotation for zebrafish
RNA-Seq
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
2
votes
2
replies
1.3k
views
Telomere sequence in ncbi human genome assembly?
telomere sequencing dnaseq sequence ttaggg
4.4 years ago by eva_u ▴ 30
0
votes
6
replies
3.0k
views
filtering on F_PASS(GT="het") in bcftools gives contradictory results
SNP filtering bcftools
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 60
2
votes
4
replies
1.4k
views
Single-cell RNAseq for glia
RNA-Seq rna-seq sequencing
updated 4.5 years ago by ★ 1.1k • written 4.6 years ago by • 0
5
votes
5
replies
3.9k
views
nextflow set tuple issue
software error
4.5 years ago by JoeDoasi ▴ 10
1
vote
3
replies
2.3k
views
Facing issue while installing Bio::SeqIO module
bioseqIO
updated 4.5 years ago by 45k • written 4.6 years ago by • 0
1
vote
4
replies
956
views
Whole Genome Sequencing: Identification of genomic differences
genome
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 10
0
votes
0
replies
892
views
FitHiChIP issue input file
next-gen HIChIP
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
3
votes
2
replies
1.2k
views
Data access through python
SNP ExAC ANNOVAR refGene python
updated 4.5 years ago by 153k • written 4.6 years ago by • 0
0
votes
2
replies
1.2k
views
Why I can't download gtf files from GenCode
gene R
updated 4.5 years ago by 153k • written 4.6 years ago by • 0
0
votes
2
replies
1.9k
views
FASTQ,BAM and VCF file size for 300X WES samples
next-gen sequencing storage
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 10
0
votes
0
replies
960
views
Gatk spark beta
gatk genome spark
4.5 years ago by quentin54520 ▴ 120
0
votes
2
replies
1.6k
views
How to align zebrafish RNA-seq data against a reference genome with splice sites using hisat2?
hisat2 zebrafish alignment RNA-Seq fastq
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 30
1
vote
1
reply
1.1k
views
how to determine low quality variants in vcf files
vcf variant_depth
4.5 years ago by pt.taklifi ▴ 70
7
votes
17
replies
5.8k
views
Sciclone on exome sequencing data
sciclone exome seq copy number
updated 4.6 years ago by 20 • written 9.5 years ago by ▴ 160
2
votes
3
replies
5.9k
views
where can I download convertf (to convert vcf/plink files into eigenstrat)
eigenstrat convertf
updated 2.2 years ago by 45k • written 7.9 years ago by ▴ 100
0
votes
0
replies
737
views
Graphtyper vs GATK
Graphtyper GATK
4.6 years ago by Friyunnwoo ▴ 20
0
votes
0
replies
887
views
How to compare two datasets of proteomic analysis when there are unique and common proteins?
proteomics mass spectrometry protein replication
4.6 years ago by Farah ▴ 80
121,913 results • Page 701 of 2439
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Comment: Why is academic software hard to install?
A: Concatenate multiple MUSCLE alignment result to build a phylogenetic tree
Comment: Different UMAP for batch correction in R and Pytho
Getting VCF file for the 1000 genome project with rsid
Answer: Different UMAP for batch correction in R and Pytho
Answer: Different UMAP for batch correction in R and Pytho
Answer: Different UMAP for batch correction in R and Pytho
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Recent Replies
Comment: Concatenate multiple MUSCLE alignment result to build a phylogenetic tree by san96 ▴ 190
Hi Mensur, sorry for this but I'm a little stuck. I’m trying to build a species tree for the first time and I would like to clarify a few …
Comment: Tried building a compact sequence format with 4-bit storage by Alex Reynolds 36k
In addition to looking at other tools as a baseline: https://en.wikipedia.org/wiki/Compression_of_genomic_sequencing_data maybe also look i…
Comment: Different UMAP for batch correction in R and Pytho by Madiha ▴ 20
Thanks, António for a helpful, detailed response. I didn't take into consideration that the plotting order of cells from each batch can be …
Comment: [vg giraffe] Unable to add read group to BAM file by saruman • 0
It seems that using the following format fixes the problem: --read-group "1 SM:HG002 LB:lib1 PL:illumina PU:unit1" As shown below: …
Comment: Developing a genomics ML model using bytes? by dariober 15k
> what if we can use the bytes to develop a model? My understanding is that the OP is considering building a model using the sequences in …
Comment: WGCNA package in R: dendogram plot error by RJ • 0
You might had delete the outliers from the expression table but then the traits data.frame doesn't match with expression table dimensions.
Comment: miRNA low mapping ratings by Ant ▴ 50
No, it's a personal dataset. I haven’t seen the link, but if I understand correctly, it's not possible to use the software for free, right?
Comment: miRNA low mapping ratings by GenoMax 153k
So this is a public dataset? QIAseq miRNA libraries may require special handling. Have you seen --> https://resources.qiagenbioinformatics.…
Comment: Trouble when installing arb by GenoMax 153k
Are you referring to software found here --> http://download.arb-home.de/release/latest/ ? If so why are you installing the source. Authors…
Comment: Hifiasm is getting killed while trying to assemble a genome by GenoMax 153k
All valid points. This is a SRA dataset. If it is covered by a publication hopefully it is not a bad one. @Pranav if you can post the SRA a…
Answer: Different UMAP for batch correction in R and Pytho by antonioggsousa 3.4k
Hi, I'm mostly an R user, but the codes you presented look correct to me. The two UMAP projections *"look too similar to be different"*, …
Answer: How to properly assemble phage genomes? by Joe 22k
This might help: https://millardlab.org/lab-members/alumni/lucy-gannon/lucys-beginner-guide-to-bacteriophage-genome-assembly/
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Thanks for your reply. Yes it's single-cell and we're talking about roughly 30 pre-selected genes. I see. I was rather referring to the d…
Answer: Best set of tools / workflows for predicting the biosynthesis pathways of comple by Joe 22k
This may not be exactly what you're looking for (kind of the other way around, predicting synthetic clusters from genes rather than the pro…
Comment: Developing a genomics ML model using bytes? by ATpoint 89k
How is this different from https://www.biostars.org/p/9615062/
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