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1,000 results • Page 4 of 20
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5
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8
replies
623
views
Multiple threads on ubuntu server
Ubuntu
updated 3 months ago by 6.4k • written 3 months ago by ▴ 50
1
vote
8
replies
2.6k
views
subset data problem
R seurat
9 months ago by Andy ▴ 120
0
votes
8
replies
10.0k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 10 months ago by 43k • written 6.8 years ago by • 0
0
votes
8
replies
1.5k
views
VCF samtools
vcf samtools variant-calling
updated 10 months ago by 43k • written 2.4 years ago by • 0
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 9.6 years ago by • 0
5
votes
8
replies
2.5k
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
updated 9 months ago by ▴ 460 • written 15 months ago by • 0
0
votes
8
replies
666
views
Phobius error: Could not read provided fasta sequence at phobius.pl line 408
Phobius
updated 9 weeks ago by ▴ 10 • written 3 months ago by ▴ 30
0
votes
8
replies
579
views
STAR aligner options
STAR
5 weeks ago by theophile • 0
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 4 days ago by • 0 • written 5.1 years ago by 11k
2
votes
8
replies
705
views
TCGA Biospecimens Slides Extraction
tcga
updated 10 weeks ago by ★ 1.2k • written 11 weeks ago by ▴ 10
0
votes
8
replies
1.5k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools MarkDuplicates
updated 7 weeks ago by • 0 • written 19 months ago by • 0
1
vote
8
replies
1.5k
views
counts of cite-seq-count vs. cellrenager varies tremendously
citeseq-count cellranger cite-seq scRNA-seq
updated 4 months ago by 82k • written 9 months ago by ★ 1.8k
3
votes
8
replies
1.0k
views
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
BLAST bowtie2 BWA alignment
9 months ago by cheesefish21 ▴ 10
1
vote
8
replies
995
views
Reads in IGV are mostly in intron regions
Patchseq RNA-seq
10 months ago by Kai_Qi ▴ 130
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter genome
updated 11 months ago by 43k • written 4.6 years ago by ▴ 120
6
votes
8
replies
1.2k
views
conda: command not found: gatk.
conda gatk
11 months ago by bestone ▴ 30
1
vote
8
replies
3.9k
views
No gene can be mapped
R GSEA
updated 4 months ago by ★ 1.8k • written 2.3 years 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
3
votes
8
replies
926
views
Can these RNAseq runs be combined?
transcriptomics replicates RNAseq
updated 10 months ago by 142k • written 10 months ago by • 0
2
votes
8
replies
998
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature HGVS
updated 10 weeks ago by ▴ 560 • written 4 months ago by 4.2k
4
votes
8
replies
618
views
GCP Snakemake
snakemake GCP
updated 3 months ago by 43k • written 3 months ago by ▴ 10
5
votes
8
replies
1.0k
views
sc-RNA seq pipeline
scRNA-seq NGS RNA-Seq
4 months ago by Researcher ▴ 30
2
votes
8
replies
484
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
18 hours ago by Qroid ▴ 40
5
votes
8
replies
2.0k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq DNA-Seq contamination QC
updated 6 months ago by • 0 • written 3.7 years ago by ▴ 230
5
votes
8
replies
1.9k
views
snpeff install error
snpeff
updated 12 months ago by 43k • written 12 months ago by ▴ 30
1
vote
8
replies
1.2k
views
Shannon's Entropy by Sliding Window in R
Sequence Window R Entropy Sliding
updated 11 months ago by ▴ 850 • written 17 months ago by • 0
1
vote
8
replies
848
views
DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment
rna-seq deseq2
5 months ago by pingu77 ▴ 20
3
votes
8
replies
2.0k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 11 months ago by 43k • written 5.5 years ago by • 0
0
votes
8
replies
4.5k
views
Downloading single cell data from NCBI
ncbi rna-seq fastq-dump single-cell
updated 8 months ago by 43k • written 5.4 years ago by ▴ 380
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 27 days ago by • 0 • written 4.7 years ago by ▴ 180
4
votes
8
replies
1.8k
views
Error while running nf-core/rnaseq pipeline
nf-core RNA-seq
11 months ago by eesha28112001 • 0
1
vote
8
replies
2.5k
views
Using NCBIs EDirect to download pubmed abstract
edirect pubmed NCBI
updated 10 months ago by 43k • written 5.9 years ago by • 0
0
votes
7
replies
930
views
Mugsy error -directory must be a directory
Mugsy
updated 7 months ago by 43k • written 3.4 years ago by ▴ 160
0
votes
7
replies
2.6k
views
How to perform gene annotation in kallisto?
Gene kallisto annotation
updated 8 months ago by • 0 • written 2.7 years ago by ▴ 100
3
votes
7
replies
1.1k
views
Use giraffe in vg
giraffe vg
updated 9 months ago by ▴ 460 • written 10 months ago by • 0
0
votes
7
replies
763
views
Search for specific SNPs in VCF files of patients.
ANNOVAR vcftools bcftools GATK VCF
updated 4 months ago by 43k • written 4 months ago by ▴ 10
0
votes
7
replies
1.6k
views
Comparing the GVF file & VCF file
gvf dna vcf ensembl ngs
updated 5 months ago by • 0 • written 15 months ago by ▴ 30
3
votes
7
replies
2.2k
views
align_and_estimate_abundance error Trinty
align_and_estimate_abundance RNA-SEQ RSEM Trinity
updated 11 months ago by 43k • written 2.6 years ago by ▴ 60
2
votes
7
replies
909
views
Removing duplicates
duplicates ONT minimap2
updated 18 days ago by ▴ 580 • written 20 days ago by • 0
1
vote
7
replies
1.2k
views
For loop STAR not working
RNA-Seq STAR
updated 10 months ago by 43k • written 2.9 years ago by ▴ 30
1
vote
7
replies
894
views
help with weird PCA? (vcfR)
vcftools vcfR R
5 months ago by MaeBH • 0
0
votes
7
replies
536
views
SNP calling with many samples using bcftools
bcftools SNP multithreading
5 months ago by George ▴ 10
2
votes
7
replies
527
views
How to predication/annotation trans-splicing in genome
trans-splicing genome annotation mitochondrial
3 months ago by oasiswho • 0
1
vote
7
replies
1.6k
views
Accuracy of Methods for Gene Variant Detection and Quantification: Kallisto Pseudoalignment vs. STAR Alignment
kallisto STAR RNA-seq Transcript_variants
11 months ago by sohail.mbio • 0
0
votes
7
replies
391
views
single nuclei sequencing questions
fastq single-nuclei-sequencing
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
7
votes
7
replies
608
views
6 follow
PCA plot interpretation (single population)
PCA GWAS pruning
3 months ago by Shane ▴ 20
0
votes
7
replies
1.2k
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA Expression mRNA
updated 11 months ago by 4.2k • written 11 months ago by ▴ 40
2
votes
7
replies
693
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq contamination
updated 7 weeks ago by ▴ 390 • written 7 weeks ago by ▴ 20
3
votes
7
replies
517
views
How does kallisto handle multi mapped reads?
kallisto
updated 10 weeks ago by ★ 6.0k • written 10 weeks ago by ▴ 150
0
votes
7
replies
1.1k
views
Tool-Compare Sequences within a Single Tree.
mutations sequence alignment
updated 10 months ago by 43k • written 5.2 years ago by • 0
1,000 results • Page 4 of 20
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The Biostar Herald for Monday, May 06, 2024
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Comment: Is therer any suggestions on mapping rate of WGBS data?
Answer: plotting PCA PLINK eigenvec output in R
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A: PCA in a RNA seq analysis
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Comment: trying to count a pattern in my fastq file using bbduk by GenoMax 142k
I don't think you can use N's in `literal=` since the match is literal as the option says. Depending where in the read this pattern is you …
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https://www.biostars.org/u/98332/ : This may be best posted as a new question since you are now running into a problem with tool usage.
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If rRNA genes have been mistakenly assigned to these genes, could it be expected that the percentage of ribosomal genes(rpl,rps) would be …
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Mapping rate for bisulfite data is typically worse because of reduced complexity of the sequences. The efficiency will depend on your read …
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In your paper, you mentioned that a normalization value of 0 for Malat1 is also indicative of a low-quality cell. But what if the dropout e…
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Thank you. But can we say that this is biologically informative ? If this gene had been detected in excess specifically within a single c…
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$20,000 for the first Prize?XD
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Why does your question sound like an assignment (if it's not, reformulate it, note you are in no position to give the volunteers here assig…
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Hi, Thank you for your contribution, here is your *free* code review: - This scenario is sort of ideal for a snakemake workflow and I th…
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