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121,625 results • Page 619 of 2433
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5
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3
replies
2.0k
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bioawk looping to retrieve fasta sequences by seq ID pattern
regex fasta bioawk loop
updated 4.1 years ago by 88k • written 4.1 years ago by ▴ 20
3
votes
3
replies
1.9k
views
Best pre and post alignment / variant calling QC tools for many WGS/RNA samples 2021
fastq vcf bam
4.1 years ago by William ★ 5.4k
2
votes
7
replies
2.1k
views
Human genome hg19 variant calling with bcftools
bcftools samtools variant-calling
updated 2.6 years ago by 45k • written 4.1 years ago by • 0
0
votes
2
replies
1.4k
views
Subset cells by ADT expression
10x adt seurat
4.1 years ago by chi.delta ▴ 40
8
votes
5
replies
1.5k
views
Bioinformatics Definitions
genome
updated 4.1 years ago by ★ 2.9k • written 4.1 years ago by ▴ 70
0
votes
0
replies
604
views
GAPIT Genomic selection using ECMLM
GAPIT Genomic Selection
4.1 years ago by sssss • 0
0
votes
0
replies
1.6k
views
DiffBind Error in if (file.info(peaks)$size > 0) { : missing value where TRUE/FALSE needed
diffBind
4.1 years ago by alexmondaini ▴ 20
2
votes
1
reply
840
views
Extract locus length given locus accession number
genome ncbi API
updated 4.1 years ago by 152k • written 4.1 years ago by ▴ 120
0
votes
0
replies
569
views
Differential expression of microRNAs
Differentally microRNA expressed
updated 4.1 years ago by 88k • written 4.1 years ago by • 0
0
votes
7
replies
2.3k
views
Salmon Quant /SubRead featureCounts Results Total Aligments:0
Annotation Genome HG38 Rna-Seq SubRead
4.1 years ago by santos48 ▴ 40
0
votes
2
replies
1.4k
views
How to export a table from SAS software to Excel
SAS
updated 4.1 years ago by 166k • written 4.1 years ago by ▴ 20
0
votes
0
replies
716
views
Random effect with LMM in EWAS
LMM fixed-effect random-effect EWAS GWAS
updated 11 months ago by 45k • written 4.1 years ago by ▴ 30
1
vote
4
replies
1.6k
views
HISAT2 error message :Could not locate a HISAT2 index corresponding to basename "/mnt/c/mkr-index2/mm10_adera/genome"
hisat2
updated 4.1 years ago by 88k • written 4.1 years ago by ▴ 80
0
votes
0
replies
1.7k
views
Job: Research Scientist Bioinformatics (Germany, full-time, permanent)
research-scientist
updated 2.1 years ago by 45k • written 4.1 years ago by ▴ 120
0
votes
3
replies
1.7k
views
Discussion: Clinical genetics germline variants detection pipeline
NGS GATK clinical pipeline genetics
updated 4.1 years ago by 88k • written 4.1 years ago by ▴ 60
0
votes
0
replies
667
views
GATK SortSamSpark error: Failed to load org.broadinstitute.hellbender.Main
sortsamspark spark gatk
4.1 years ago by dragon940401 • 0
3
votes
2
replies
1.5k
views
How to activate and install bioinformatics software
Biostar-handbook
updated 2.5 years ago by 45k • written 4.1 years ago by ▴ 20
5
votes
6
replies
1.8k
views
Forum: Suggestion of Biostatistics book.
RNA-SEQ R Biostatics
updated 4.1 years ago by ★ 2.9k • written 4.1 years ago by ▴ 30
3
votes
2
replies
1.2k
views
How to know the positions of contigs in a reference genome
mapping positions alignment reference genome contigs
updated 4.1 years ago by 152k • written 4.1 years ago by ▴ 20
0
votes
0
replies
635
views
how can I analyse gender spesific CNV analysis with CNVkit?
diagram gender CNV CNVkit log2
4.1 years ago by enes ▴ 40
0
votes
4
replies
1.2k
views
extract the ids and key values
extract grep
updated 4.1 years ago by 9.3k • written 4.1 years ago by ▴ 80
0
votes
0
replies
862
views
liftover results usage: input bed file and output bed file have different rows, how can I link coordinates between input and output files?
unmapped liftover coordinates relationship
4.1 years ago by wangjinpeng0225 ▴ 30
2
votes
3
replies
2.9k
views
cutadapt: error: unused arguments //not recognizing my sequences when using a loop?
cutadapter
4.1 years ago by Kirsten • 0
1
vote
4
replies
1.4k
views
Divide the genome to vary lengths windows in R
bedtools R BED
updated 4.1 years ago by 45k • written 4.1 years ago by ▴ 40
3
votes
4
replies
1.3k
views
plink2 cannot identify options when looping the chromosomes
plink2 plink
4.1 years ago by okiedokie1208 ▴ 40
2
votes
10
replies
2.8k
views
How to search for genes 100Kb up and downstream of any genomic site
R
updated 4.1 years ago by 36k • written 4.1 years ago by ▴ 50
1
vote
1
reply
685
views
How to extract genes from RNA-seq using its reference genome?
of alignment RNAseq genes list
updated 4.1 years ago by 152k • written 4.1 years ago by • 0
0
votes
0
replies
673
views
CHIPQC problem ( the wrong ReadL and no FragL RelCC)
CHIPQC
updated 4.1 years ago by 152k • written 4.1 years ago by • 0
0
votes
3
replies
3.0k
views
WGCNA: scale-free topology fit indexes are negative
gene r WGCNA
updated 4.1 years ago by 3.9k • written 4.1 years ago by ▴ 10
6
votes
8
replies
2.7k
views
what are the reasons to find so few Differentially expressed genes (DEGs)?
Gene RNA
updated 4.1 years ago by 15k • written 4.1 years ago by ▴ 1000
0
votes
0
replies
644
views
extract exons/introns from multiple fasta files with gene sequences
intron splicing fasta CDS exon
4.1 years ago by ramiroricardo • 0
0
votes
1
reply
1.9k
views
Plink: --keep flag
--keep subset plink
updated 4.1 years ago by 11k • written 4.1 years ago by • 0
1
vote
3
replies
1.5k
views
Error when searching for matches using the PSSM score with proteins (.motif BioPython)
protein motif python biopython
2.9 years ago by Agenor Neto ▴ 10
2
votes
2
replies
1.0k
views
Detecting RNA Editing in Single-Cell RNA-seq
scRNAseq RNAediting
4.1 years ago by fouerghi20 ▴ 80
3
votes
3
replies
1.4k
views
Intrinsically disordered region(IDR) or Intrinsically disordered Protein(IDP)
biopython
updated 4.1 years ago by 22k • written 4.1 years ago by • 0
0
votes
3
replies
3.1k
views
STARsolo --EmptyDrops_CR parameters
RNA-seq alignment STAR
updated 3.5 years ago by • 0 • written 4.1 years ago by ▴ 70
3
votes
3
replies
3.6k
views
Nanopore tutorial for beginners
nanopore
updated 2.4 years ago by 45k • written 4.1 years ago by ★ 1.3k
0
votes
0
replies
547
views
Mitochondrial targeting sequence
mts crispr geneediting gene Sequence
4.1 years ago by chiti.agarwal ▴ 10
3
votes
2
replies
3.3k
views
tools for identifying mitochondrial-targeting sequence in different proteins
alignment sequencing mtp
updated 2.8 years ago by 45k • written 10.0 years ago by ▴ 50
9
votes
6
replies
9.8k
views
6 follow
Quadruplex sequence batch prediction
Quadruplex
updated 2.5 years ago by 45k • written 10.2 years ago by ▴ 50
0
votes
0
replies
579
views
Read distribution tool accounting for read orientation
RNA
4.1 years ago by VHahaut ★ 1.2k
2
votes
1
reply
948
views
Different ab initio 3D structure prediction for same protein sequence by trRosetta
3D protein trRosetta structure prediction
updated 4.1 years ago by ▴ 390 • written 4.1 years ago by ▴ 80
0
votes
3
replies
1.3k
views
Local realignment around indels
local realignment
4.1 years ago by Elisa • 0
1
vote
5
replies
3.0k
views
How to create a proper design matrix/contrast matrix for methylation 850k analysis in limma?
850k methylation analysis R limma design matrix
updated 4.1 years ago by • 0 • written 5.5 years ago by ▴ 140
2
votes
5
replies
4.3k
views
Snakemake error: "Removing output files of failed job since they might be corrupted:"
Snakemake
updated 4.1 years ago by 15k • written 4.1 years ago by ▴ 100
2
votes
5
replies
5.0k
views
Beagle: Skip intervals with no common markers
beagle plink vcf conformgt
updated 4.1 years ago by ▴ 20 • written 5.4 years ago by ▴ 10
1
vote
0
replies
634
views
Duplicate genotypes after phasing in Beagle
Beagle Phasing
4.1 years ago by PKW ▴ 110
1
vote
0
replies
1.1k
views
Deeptools plotPCA on RNA-seq help
PCA deeptools RNAseq
4.1 years ago by jrichardalbert ▴ 10
1
vote
2
replies
1.1k
views
How to perform differential expression on proteomics data?
proteomics TMT Differential-Expression R
4.1 years ago by lenC_biotecLover ▴ 90
2
votes
6
replies
3.3k
views
How to find overlapping coordinates of a gtf file
gtf-file sequencing genome annotation RNA-Seq
updated 4.1 years ago by 36k • written 4.1 years ago by ▴ 320
121,625 results • Page 619 of 2433
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Answer: How do I generate synthetic 16S RNA gene sequences?
Answer: Does edgeR supports random effects?
Answer: Tools for bulk RNA-seq celltype deconvolution
How do I generate synthetic 16S RNA gene sequences?
Comment: Intro + Question
Comment: Draw a genome map with CGView server?
A: single cell RNA seq Differential Expression using MAST
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Recent Replies
Comment: Tools to view fastq file by GenoMax 152k
`FinchTV` is meant for use with ABI chromatogram (sanger sequencing) files. Don't think it can read fastq files. In any case there is no ca…
Comment: Does edgeR supports random effects? by Gordon Smyth ★ 8.2k
Subsetting to half the data will obviously change the results. The mean-variance relationship and the inter-block correlation need to be re…
Answer: Tools to view fastq file by chuckles • 0
Obviously a very late response, here, but for anyone looking for answers now or in future: I'm sure there are other tools, but the one I…
Answer: how extract CpG methylatiuon calls from nanopore long sequencing bam file ? by Istvan Albert 102k
The BAM file has tags that contain the information you need. There are tags such as: * `MM`: Modified base motif and positions. …
Comment: Does edgeR supports random effects? by 406339165 ▴ 10
**The code was super helpful — thank you so much, Gordon! (cc: @gordonsmyth)** I ran the code and got the following results, but I’m a bit…
Comment: STAR alignment to small fasta file failing by GenoMax 152k
I suggest that you give another (bbmap, bwa-mem2, bowtie etc) NGS aligner a try. STAR is splice-aware and likely has default options that l…
Comment: Significance of the term "tile" in sequencing? by Ram 45k
Open a new question, add the detail you just gave GenoMax in that question, then delete this answer.
Comment: Significance of the term "tile" in sequencing? by Christopher ▴ 10
It's from NovaSeq6000
Comment: Significance of the term "tile" in sequencing? by Christopher ▴ 10
Okay, I apologize. Since I saw that this issue had already been mentioned in the forum, I thought it wasn’t necessary to create a new topic…
Answer: How do I generate synthetic 16S RNA gene sequences? by shelkmike ★ 1.7k
Maybe, the following is worth doing:<br> 1) First, you need to understand how much the natural sequences differ from the covariance model. …
Comment: STAR alignment to small fasta file failing by Annie • 0
There are 8 reference sequences in the fasta, total about 9,000 bases. I'm using STAR because it's what I've been using for these data and …
Comment: How do I generate synthetic 16S RNA gene sequences? by Max Sikolenko ▴ 70
> Why do you need to augment 16S rRNA sequences, given that tens of millions are already available? If your main reason is sequence diversi…
Comment: Draw a genome map with CGView server? by Max Sikolenko ▴ 70
Circular genome maps of unassembled contigs do not make much sense, unfortunately. Anyway, > Which tools should I use for drawing bacteria…
Answer: Minimap2 Output by Istvan Albert 102k
Minimap 2 has two outputs the PAF format and the SAM format. Each has a documentation that describes how the information is encoded. In …
Comment: Intro + Question by Pierre Lindenbaum 166k
how about just asking this kind of questions in their github repo ?
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