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1,000 results • Page 3 of 20
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Python3 or Ubuntu, not perl: Have Primers with Degenerate Bases, Need tool or way to List all Possible Nucleotide Sequences
degenerate-bases python primers biopython
updated 7 weeks ago by ★ 1.7k • written 7 weeks ago by • 0
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome base-calling fastq nanopore
updated 2 days ago by 43k • written 8 months ago by • 0
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
3
votes
9
replies
798
views
Understanding this analysis pipeline
reads
updated 10 months ago by 43k • written 10 months ago by • 0
3
votes
9
replies
1.7k
views
How to get negative training set if I don't know what constitutes negative?
machine-learning dna-sequence blast
updated 5 months ago by 43k • written 7.6 years ago by • 0
0
votes
9
replies
1.5k
views
Chipseq analysis on repeat genes
galaxy repeatmasker ChIP-seq repeat-elements ATAC-seq
updated 7 months ago by ▴ 900 • written 7 months ago by ▴ 10
6
votes
9
replies
2.9k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool Cellranger NCBI
updated 10 months ago by 43k • written 2.3 years ago by ▴ 20
0
votes
9
replies
995
views
gene id
gene-id NCBI
updated 10 months ago by 141k • written 10 months ago by • 0
0
votes
9
replies
1.1k
views
grep multiple lines form file
shell-script grep
updated 10 months ago by 43k • written 4.0 years ago by ▴ 30
2
votes
9
replies
7.6k
views
6 follow
Read MAP and PED files in PLINK
GWAS PLINK
updated 4 months ago by 141k • written 6.0 years ago by • 0
1
vote
9
replies
4.4k
views
Unable to install bioconda and bowtie
bioconda conda
updated 4 months ago by 13k • written 19 months ago by ▴ 30
0
votes
9
replies
845
views
Deseq2 error
R deseq2
7 months ago by sgadila • 0
1
vote
9
replies
670
views
Htseq-count reads with missing mate encountered
htseq htseq-count
5 months ago by Bjorn • 0
1
vote
9
replies
630
views
Problem with ONT sequencing pipeline. Probably in the Samtools part
bam samtools ONT
updated 3 months ago by 141k • written 3 months ago by • 0
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
3
votes
9
replies
982
views
Estimate sizes of repeats in a especific Gene
CGG Fragile-X
11 months ago by Rafael ▴ 10
4
votes
9
replies
1.2k
views
Snakemake issue with wrappers
Python Snakemake
5 months ago by Begonia_pavonina ▴ 150
1
vote
9
replies
1.5k
views
blast retrieves "N/A" for taxonomic data
blast blastn
updated 7 weeks ago by • 0 • written 3.4 years ago by ▴ 50
2
votes
9
replies
860
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 8 days ago by 4.2k • written 6 months ago by • 0
0
votes
9
replies
5.4k
views
Calculating FPKM and TPM by hand from htseq-count output?
RNA-Seq rna-seq htseq FPKM TPM
updated 8 months ago by 82k • written 5.0 years ago by ▴ 210
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling single-cell scRNA-seq batch-effect
updated 15 days ago by 43k • written 3.9 years ago by ▴ 20
0
votes
9
replies
1.7k
views
WCGNA to Cytoscape
wgcna cytoscape rna-seq
updated 12 weeks ago by 43k • written 3.7 years ago by ▴ 40
0
votes
9
replies
608
views
99.9999% of Q30 bases is normal?
RNA-seq fastp
updated 20 days ago by 4.2k • written 21 days ago by ▴ 20
7
votes
9
replies
1.1k
views
Calculation of TMB on gene level
genomics
updated 7 months ago by ▴ 680 • written 7 months ago by ▴ 20
1
vote
9
replies
900
views
Command line or python RNA-seq read simulator
simulation RNA-seq
5 months ago by i.sudbery 19k
3
votes
9
replies
690
views
STARsolo seg fault without readMapNumber flag
STAR RNA-seq STARsolo Velocyto
updated 6 months ago by 43k • written 6 months ago by ▴ 420
1
vote
9
replies
544
views
miRNA alignment with Bowtie2
bowtie2
6 weeks ago by Chironex ▴ 40
1
vote
9
replies
1.0k
views
gene annotation
gtf gene-annotation
updated 11 months ago by 43k • written 11 months ago by • 0
1
vote
9
replies
1.2k
views
Trying to edit VCF file
VCF R bcftools snpsaurus
updated 11 months ago by 43k • written 11 months ago by • 0
1
vote
9
replies
623
views
Approach for multi species comparative transcriptomics and differential expression analyses
DE RNA-seq transcriptomics
updated 3 months ago by ★ 1.9k • written 3 months ago by • 0
0
votes
9
replies
1.4k
views
Samtools sam to bam error
samtools
updated 6 months ago by • 0 • written 2.0 years ago by ▴ 10
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
1
vote
8
replies
2.5k
views
subset data problem
R seurat
9 months ago by Andy ▴ 120
3
votes
8
replies
634
views
Huge decrease of BUS records using bustools
single-cell bustools 10X
9 weeks ago by julien.wollbrett • 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 9.5 years ago by • 0
0
votes
8
replies
1.9k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython python
updated 11 months ago by 43k • written 4.4 years ago by • 0
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
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq deseq2
updated 10 months ago by 43k • written 3.9 years ago by ▴ 60
3
votes
8
replies
2.0k
views
Kallisto mapping paired end
Kallisto mapping
updated 11 months ago by 43k • written 2.2 years ago by ▴ 20
0
votes
8
replies
9.9k
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
5
votes
8
replies
1.9k
views
snpeff install error
snpeff
updated 11 months ago by 43k • written 12 months ago by ▴ 30
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 21 days ago by • 0 • written 4.7 years ago by ▴ 180
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
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence RNA-Seq RPKM Fold-Change batch-effect
updated 14 days ago by 43k • written 7.0 years ago by ▴ 20
0
votes
8
replies
356
views
Error in cnetplot enrichplot package
R
updated 9 days ago by 43k • written 9 days ago by • 0
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
1.9k
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 3 months ago by ★ 16k • written 3 months ago by • 0
1
vote
8
replies
987
views
Reads in IGV are mostly in intron regions
Patchseq RNA-seq
10 months ago by Kai_Qi ▴ 130
1
vote
8
replies
1.1k
views
Mitochondrial genes - TPM calculation bulk RNA-Seq
TPM RNA-Seq mtDNA
5 months ago by nick_b55 ▴ 10
4
votes
8
replies
613
views
GCP Snakemake
snakemake GCP
updated 3 months ago by 43k • written 3 months ago by ▴ 10
1,000 results • Page 3 of 20
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C: TOPGO- how to do GO enrichment using a custom go database?
Answer: NGS forensics: how to know if data is fabricated
Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
Comment: DESeq2 processing problems
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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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