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121,922 results • Page 75 of 2439
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1
vote
7
replies
2.6k
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Core_nt database not available to download?
blast ncbi
updated 13 months ago by 153k • written 13 months ago by ▴ 260
0
votes
0
replies
496
views
News: Course in Italy: Introduction to Statistics in R (30 September to 3 October 2024)
R GLM Statistics GLMM
13 months ago by Physalia-courses ★ 2.6k
4
votes
3
replies
1.1k
views
Rapid K-mer search
search k-mer
updated 13 months ago by 8.7k • written 13 months ago by ▴ 850
0
votes
2
replies
782
views
Restrictive alignment with minimap2
nanopore alignment minimap2
13 months ago by njornet ▴ 20
0
votes
1
reply
756
views
Generating a Python parsable local db from dbSNP
Python
updated 13 months ago by ▴ 540 • written 13 months ago by ▴ 130
3
votes
1
reply
711
views
TPM normalization of counts
TPM featurecounts
13 months ago by analyst ▴ 70
0
votes
4
replies
1.2k
views
Nr Database just for Prokaryotes
nr database
updated 12 months ago by 153k • written 13 months ago by ▴ 20
0
votes
0
replies
422
views
I encounter a problem while checking my MaGeck results.
MaGeck
13 months ago by Pallondyle • 0
2
votes
7
replies
1.8k
views
How to check coverage in bam file?
bam
updated 13 months ago by ★ 4.3k • written 13 months ago by ▴ 60
0
votes
0
replies
407
views
DiffBind for MBD-seq
DiffBind MBD-seq
13 months ago by mariannapauletto ▴ 90
1
vote
2
replies
812
views
Germline and somatic SNPs in same or different allele
germline vcf phasing somatic
13 months ago by Nacho del Valle • 0
4
votes
5
replies
1.6k
views
Extracting human exome from GTF file
gtf human exons
updated 13 months ago by 103k • written 13 months ago by • 0
0
votes
0
replies
428
views
AlphaFold3 molecular docking
alphafold3 ligand moleculardocking
13 months ago by iamsmor • 0
1
vote
4
replies
2.2k
views
Is it Necessary to Use Raw Data for SCTransform When Regressing Out Cell Cycle Genes?
SCTransform
13 months ago by Kimaya • 0
4
votes
6
replies
1.4k
views
Batch correction preserving biological difference
scRNA-Seq batch-correction
13 months ago by noodlejackson ▴ 40
1
vote
2
replies
974
views
Analyzing RNA-seq data with Salmon
quantifying RNAseq data countmatrix Salmon
13 months ago by Eduardo Oñate • 0
0
votes
1
reply
556
views
Opposite REF and ALT alleles
reference-allele eqtl alternative-allele Gwas
updated 13 months ago by 45k • written 13 months ago by • 0
0
votes
0
replies
368
views
(metagenomic) Bins exceeding genome in length
Binning Metagenomic
13 months ago by alenew.am ▴ 10
0
votes
0
replies
577
views
News: Online course - Shotgun Metagenomics: Processing and Analysis
Prokka MetaPhlAn Metagenomics StrainPhlan PanPhlAn
updated 13 months ago by 45k • written 13 months ago by ★ 2.6k
12
votes
6
replies
3.2k
views
Downloading paired end fastq data from SRA
SRA single-cell RNA-Seq
13 months ago by Matheus • 0
0
votes
3
replies
814
views
Find the CDS region of the gene we are interested in in multiple unannotated genomes
genome cds bioinformation
updated 13 months ago by 153k • written 13 months ago by ▴ 20
0
votes
0
replies
378
views
Functional normalization using minfi::preprocessFunnorm and control PCs in later analyses
normalization EWAS epigenome preprocessing
updated 13 months ago by 45k • written 13 months ago by • 0
0
votes
0
replies
295
views
Package to design fragment tiling library
protein
13 months ago by ar_nabbi • 0
4
votes
4
replies
2.2k
views
How to understand differences in duplication rates between picard MarkDuplicates and fastp
duplication-rate rna-seq fastp picard
13 months ago by Assa Yeroslaviz ★ 1.9k
3
votes
5
replies
1.2k
views
Compatibility of IonTorrent BAM Files for HRD Analysis with nf-core/oncoanalyser
nf-core HRD IonTorrentPlatform ngs oncoanalyser
13 months ago by Nour-eddine ▴ 70
0
votes
0
replies
694
views
Job: Freelance Expert in Human Skin Microbiome
multiomics skin-microbiome metagenomics microbiota
updated 13 months ago by 45k • written 13 months ago by • 0
7
votes
6
replies
1.5k
views
Python for pdf reports
Cancer Python3 reports
updated 13 months ago by ▴ 140 • written 13 months ago by ▴ 20
0
votes
0
replies
371
views
Different position for same gene using annotatePeak from ChIPseeker
ChIPseeker ATACseq
13 months ago by QX ▴ 80
0
votes
0
replies
376
views
plotHeatmap from deeptools explain
atac-seq
13 months ago by QX ▴ 80
5
votes
4
replies
7.6k
views
Kraken2 with Nanopore reads
kraken2 nanopore kraken
updated 13 months ago by ▴ 80 • written 4.2 years ago by ★ 2.1k
1
vote
1
reply
768
views
Using Ensembl Gene IDs for Ontology Analysis
DAVID Ensembl Reactome Ontology-Analysis
updated 13 months ago by 5.1k • written 13 months ago by ▴ 10
1
vote
1
reply
1.5k
views
AlphaFold 3 - how to check MSA depth?
modeling protein interaction alphafold
updated 13 months ago by ★ 3.1k • written 13 months ago by ▴ 10
5
votes
2
replies
867
views
Short tandem repeat (STR) expansions identificaiton workflow from RNA-seq data
RNA-seq STR
updated 13 months ago by 45k • written 13 months ago by ★ 9.6k
0
votes
0
replies
396
views
CNVkit metrics normal range
CNVkit CNV metrics
13 months ago by Mateo • 0
2
votes
7
replies
1.9k
views
Generate Max Number of DNA Sequences separated by a given Hamming distance
hamming-distance Barcode variants DNA
13 months ago by rtrende ▴ 80
2
votes
1
reply
698
views
Canu Output Explanation
fungi canu genome assembly
updated 13 months ago by 13k • written 13 months ago by ▴ 240
3
votes
4
replies
1.1k
views
Recommendations for performing Bulk RNA sequencing on non-model organism with poor genome annotation?
RNA-seq
updated 13 months ago by ★ 1.9k • written 13 months ago by ▴ 60
2
votes
1
reply
1.5k
views
Can I use snp data for iqtree?
alignment vcf iqtree variant-calling
updated 13 months ago by 45k • written 13 months ago by • 0
5
votes
5
replies
2.2k
views
LD Pruning in GWAS
PLINK PCA pruning LD GWAS
updated 13 months ago by 4.8k • written 13 months ago by ▴ 40
0
votes
2
replies
868
views
Adapter trimming WGS Illumina DNA PCR free kit with BBduk
bbduk adapter-trimming WGS
13 months ago by omicsfury • 0
1
vote
3
replies
1.4k
views
Seeking Advice on Using `edgeR` and `variancePartition` for RNA-seq Data with Multiple Tissues and Patients
linear-mixed edgeR modeling variancePartition
updated 13 months ago by ★ 8.3k • written 13 months ago by • 0
1
vote
1
reply
696
views
How to create a phylogenetic tree
need I help some
updated 13 months ago by 22k • written 13 months ago by • 0
1
vote
1
reply
1.2k
views
Converting vg and gfa files?
gfa pangenome vg graphs
updated 13 months ago by 7.9k • written 13 months ago by ▴ 40
0
votes
0
replies
335
views
Using RSEM after Cuffcompare
RNA-seq cuffcompare RSEM
13 months ago by ZZOYEA ▴ 20
0
votes
3
replies
1.2k
views
Convert "Locus Tag" to a RefSeq ID or ENSEMBL ID
RNA-seq
updated 13 months ago by 153k • written 13 months ago by • 0
0
votes
3
replies
747
views
Single cell whole genome sequence
Single-cell WGS
updated 12 months ago by 153k • written 13 months ago by ▴ 10
0
votes
0
replies
334
views
In the absence of lncRNA annotations, how to screen out reliable lncRNA?
Synthetic plant lncRNA
13 months ago by 晨 • 0
0
votes
1
reply
767
views
Met 500 data
Somatic-variation Copy-number
updated 13 months ago by 89k • written 13 months ago by ▴ 20
0
votes
3
replies
1.0k
views
3 samples (control) vs 3 samples (condition) 100M coverage data
reads
updated 13 months ago by 89k • written 13 months ago by ▴ 60
0
votes
2
replies
1.1k
views
Explaining my heatmap for PC1 and my PC2 with gene list
pca heatmap
updated 13 months ago by 89k • written 14 months ago by • 0
121,922 results • Page 75 of 2439
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C: Annotation for gene-level analysis after stringtie
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Comment: Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken?
C: Counting Number Of Bases In A Fastq File
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Popular Question to Physalia-courses ★ 2.6k
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Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
hello @colindaven I ran the INSPECTOR tool you mentioned on the genome assemblies. Below are stats for one of my sample (othere were simi…
Comment: Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken? by Christopher ▴ 10
You are right. I initially decided to keep Cutadapt because I feel more confident using it for primer removal, and it is the tool most comm…
Answer: Help with Model by i.sudbery 22k
I'm not quite sure what you are asking. Stochastic reaction networks like this can be coded using the Gillespie algorithm. Genes being …
Comment: miRNA low mapping ratings by Ant ▴ 50
No, these are from the total reads, but when considering only the reads with adapter, I checked MultiQC again and it’s around 10–20% when a…
Comment: miRNA low mapping ratings by GenoMax 153k
> the total number of reads is very low (around 1–10% of the total reads) Are these the reads that actually have the QIAseq 3'-miRNA adapt…
Comment: Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken? by GenoMax 153k
> cutadapt > bbduk > bowtie2 > qiime2 > dada2 > kraken2 > krona Curious as to why you have `cutadapt` and `bbduk`. `bbduk` should be able…
Comment: miRNA low mapping ratings by i.sudbery 22k
As GenoMax said, the most likely thing to me here is that there is nothing cloned into the library. I can't think of any bioinformatic reas…
Comment: miRNA low mapping ratings by Ant ▴ 50
Sorry, I gave you answers based on different samples. The thing is, the total number of reads is very low (around 1–10% of the total reads)…
Comment: miRNA low mapping ratings by Ant ▴ 50
Yes, it was in 75bp. I don1t know if it was the first time he used the kit, but I remember he needs to adjust the protocol.
Comment: SNP calling with bacterial assembled genome by GenoMax 153k
> Is it possible to do this at the assembly level? By aligning to a reference you can find the differences between your assembly and the …
Comment: miRNA low mapping ratings by i.sudbery 22k
4bp would suggest there was nothing cloned into the library. But i'm a bit confused. In example in the question, it talks about 50,000 re…
Comment: miRNA low mapping ratings by GenoMax 153k
> while fewer than 100,000 reads were around 18-22 bp. That is why are you likely seeing the numbers you are observing in alignments. Wa…
Comment: Help with Model by Joe 22k
I would imagine this is something one of the AI code tools could handle.
Comment: cellranger mkref fail/error by ATpoint 89k
I think OCM = https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-3p-what-is-cellplex#on-chip Seconding to…
Comment: miRNA low mapping ratings by Ant ▴ 50
The first one it's the results from Cutadapter and the second block from miRDeep2.
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