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1,000 results • Page 4 of 20
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4
votes
8
replies
1.8k
views
Error while running nf-core/rnaseq pipeline
nf-core RNA-seq
11 months ago by eesha28112001 • 0
4
votes
13
replies
914
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 15 days ago by ★ 1.7k • written 20 days ago by • 0
4
votes
4
replies
374
views
Average expression of a sample in single-cell data
single-cell rna-seq
29 days ago by newuser2024 • 0
4
votes
3
replies
318
views
Getting less DE genes when incorporating all samples
RNA-seq differential-expression deseq2
updated 10 weeks ago by ★ 1.8k • written 10 weeks ago by ▴ 10
4
votes
16
replies
996
views
hisat2 location does not exist
hisat2
updated 9 weeks ago by 43k • written 10 weeks ago by • 0
4
votes
6
replies
959
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
4
replies
855
views
retaining only the clusters of interest
seurat single-cell scRna-seq
updated 10 months ago by 43k • written 11 months ago by • 0
4
votes
9
replies
590
views
variant calling
variant-calling
updated 28 days ago by 43k • written 29 days 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 3.2 years 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
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
847
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 29 days ago by 43k • written 5 months ago by ▴ 30
4
votes
9
replies
1.0k
views
bcl2fastq troubleshooting all reads dumped to "Undetermined"
demultiplex illumina sequencing
updated 4 months ago by 141k • written 4 months ago by ▴ 120
4
votes
7
replies
589
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 4 weeks ago by ★ 3.8k • written 4 weeks ago by ▴ 140
4
votes
6
replies
892
views
Hisat2 index and alignment question
ubuntu rna-seq index hisat2
updated 7 months ago by 100k • written 7 months ago by • 0
4
votes
7
replies
1.5k
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
6
replies
938
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
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
4
votes
5
replies
391
views
Filter out miRNA from ncRNA dataset
bowtie bowtie2 miRNA filtering ncRNA
updated 10 weeks ago by 82k • written 10 weeks ago by ▴ 10
4
votes
1
reply
1.7k
views
How does FindNeighbors() and FindClusters() related and work?
seurat clustering
updated 8 months ago by ★ 2.4k • written 8 months ago by ▴ 120
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
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 5 weeks ago by 43k • written 5.5 years ago by ▴ 110
4
votes
6
replies
1.9k
views
Failure in installing the ggtree, enrichplot, and ggtree (Bioconductor packages )
Bioconductor
updated 10 months ago by 141k • written 10 months ago by • 0
4
votes
13
replies
1.0k
views
Mapping FASTQ files of scRNA-seq to reference genome
star EBI cellranger scRNA-seq SRA
updated 3 months ago by 43k • written 4 months ago by ▴ 20
4
votes
9
replies
2.6k
views
Blast+ remote database names
blast remote databases Blastplus
updated 9 months ago by 141k • written 2.3 years ago by • 0
4
votes
5
replies
1.4k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 11 months ago by 43k • written 6.8 years ago by ▴ 750
3
votes
5
replies
1.3k
views
Running purge_dups on a hybrid assembly (optical mapping + reads)
pacbio purge_dups Assembly bionano
updated 7 months ago by 6.4k • written 3.2 years ago by ▴ 300
3
votes
7
replies
3.2k
views
vcf filter for FORMAT argument (DP/GQ/GQX > 30) multiple (380) vcf file
vcffilter vcftools sequencing
updated 10 months ago by 43k • written 4.1 years ago by ▴ 10
3
votes
1
reply
522
views
Are there pipelines to analyze the Quality Controls for ATAC-seq and ChIP-seq data?
ChIP-seq ATAC-seq
updated 9 months ago by ★ 2.9k • written 9 months ago by ▴ 180
3
votes
7
replies
1.4k
views
VG Giraffe multi-mapped reads and definition for MAPQ score
vg
9 months ago by Hendricks27 • 0
3
votes
7
replies
1.0k
views
IGV not showing bigwig track information
bigwig IGV ChIP-seq
updated 5 months ago by 82k • written 5 months ago by ▴ 10
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
3
votes
6
replies
2.1k
views
Biopython TimeExceptionError how to handle?
biopython entrez
updated 11 months ago by 43k • written 6.5 years ago by ▴ 80
3
votes
5
replies
885
views
Optimal number of features to use when integrate multi samples by Seurat in scRNAseq
scRNASeq Seurat
updated 8 months ago by 43k • written 8 months ago by ▴ 40
3
votes
5
replies
761
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run DiffBind ChIP-seq
updated 4 months ago by ★ 2.0k • written 5 months ago by ▴ 10
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 13 days ago by 43k • written 7.1 years ago by ▴ 310
3
votes
2
replies
716
views
Scvelo vs Monocle3
monocle3 scvelo
6 months ago by Chris ▴ 260
3
votes
5
replies
1.1k
views
kraken2 bacteria database 250GB+
metagenomics 16s kraken2 kraken
updated 5 months ago by 141k • written 5 months ago by ▴ 10
3
votes
8
replies
634
views
Huge decrease of BUS records using bustools
single-cell bustools 10X
9 weeks ago by julien.wollbrett • 0
3
votes
4
replies
373
views
Single cell analysis with "meta".tsv.gz file
Single-cell
29 days ago by Estevão • 0
3
votes
2
replies
1.1k
views
Creating a genotype matrix for BeviMed
snp genome Bayesian
updated 10 months ago by 43k • written 4.3 years ago by ▴ 140
3
votes
4
replies
1.0k
views
R package DESeq2 in R 3.5.1
R
updated 11 months ago by 43k • written 15 months ago by ▴ 10
3
votes
5
replies
1.5k
views
Uniprot API access to download .pdb files
PDB API Python Uniprot
11 months ago by BioGrad321 • 0
3
votes
1
reply
374
views
GEO dataset Microarray data analysis help
R microarray NCBI GEO
updated 4 months ago by 43k • written 4 months ago by ▴ 20
3
votes
2
replies
309
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics Single-Cell
updated 26 days ago by 43k • written 8 weeks ago by ▴ 20
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly Trinity RNA-seq trimmomatic
updated 10 months ago by 43k • written 8.1 years ago by ▴ 50
3
votes
6
replies
1.3k
views
how to get total read count, mapped read count and unmapped read count from multiple sam or bam files
RNAseq PYTHON R bash
updated 11 months ago by 43k • written 3.6 years ago by ▴ 460
3
votes
6
replies
1.3k
views
Busco Folder: prfl
gene genome sequencing
updated 10 months ago by 43k • written 4.2 years ago by ▴ 20
3
votes
7
replies
489
views
Snakemake rule that runs an assessment for once after completing other previous rules
snakemake
8 weeks ago by Fadlilah ▴ 10
3
votes
4
replies
3.4k
views
Switch ref/alt alleles vcf file
SNP vcf sequencing
updated 3 months ago by • 0 • written 4.4 years ago by ▴ 20
1,000 results • Page 4 of 20
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Recent Replies
Answer: Basic stats in hierfstat by mdav • 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
Comment: GATK won't produce figures while analyzing covariates to generate 'recal_plots.p by GenoMax 141k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
Comment: Post-imputation plot by kl ▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis by GenoMax 141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems by ATpoint 82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot by LChart 3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
Comment: RNA editing sites based on DNA seq and RNA seq by Adam ▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject by Adam ▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems by Adam ▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis by GenoMax 141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size Can…
Answer: cnetplot category names are too long by bkleiboeker ▴ 370
I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
Comment: Telescope issue by GenoMax 141k
You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
Comment: Mutect2 for mitochondria variant discovery by GenoMax 141k
> I keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
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