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0 votes
10 replies
2.2K views
Batch correction of two RNA-Seq data sets
deseq2 batch-correction
written by gogeni5529 • gogeni5529
0 votes
0 replies
530 views
Plot meRIP bw data on single RNA
plot merip
updated by Ram Ram • written by jia • jia
1 vote
1 reply
1.6K views
Optimal Method for Chain File Generation: BLAT vs Minimap2 and MAF2Chain vs axtChain
generation paf2chain axtchain tool chain
updated by cmdcolin cmdcolin • written by myoui3122010 • myoui3122010
0 votes
7 replies
3.3K views
Which method should I use to merge scRNA-seq data, Cellranger aggr or Seurat?
scrna-seq cellranger hdwgcna seurat
written by Apprentice Apprentice
0 votes
0 replies
513 views
Clonality dendrogram evolution
clonality clonevol dendrogram
written by alba • alba
0 votes
1 reply
2.2K views
What laptop specifications should I consider as a Bioinformatics PhD student with HPC access?
laptop hpc cluster
updated by Ram Ram • written by Tundup • Tundup
0 votes
1 reply
624 views
VCF Merge
vcf mergestr
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Muhammad • Muhammad
0 votes
4 replies
1.5K views
Script that should show if the position of an indel is within the range of a miRNA is creating empty files. Could you help me?
mirna indel
written by jhonatan.henrique • jhonatan.henrique
1 vote
2 replies
1.6K views
Issues with RAT in CAT_pack and Optimizing Relative Abundance Calculation
metagenomics taxonomy mag annotation
written by LuciaNhu • LuciaNhu
0 votes
2 replies
1.2K views
Hi-C interactions significance
chromatin interactions pvalue hi-c significance
updated by kalavattam • kalavattam • written by Helena • Helena
0 votes
4 replies
1.6K views
Conceptual and statistical help in creating a synthetic RNAseq cohort from a real-world cohort of samples
statistics deseq2 rnaseq
updated by ATpoint ATpoint • written by K.patel5 • K.patel5
0 votes
0 replies
603 views
StringTie error
de rna-seq stringtie
updated by Ram Ram • written by SHN • SHN
0 votes
0 replies
513 views
A problem with a plink file made from a VCF
plink vcf
written by HoWI • HoWI
0 votes
2 replies
1.1K views
Annotating bacterial intergenic regions
bacteria gene intergenic annotation
updated by dthorbur dthorbur • written by Gio • Gio
0 votes
0 replies
500 views
KEGGREST to retrieve some data from KEGG
genes kegglink
written by mrashad mrashad
0 votes
1 reply
859 views
Creating adjacency matrix from collapsed row values in R
adjacency reshape2 matrix r
written by ARP • ARP
0 votes
5 replies
1.6K views
Deducing AIRR-seq Library Generation From SRA Data
generation sra airflow primer airrflow
written by A Soggy Waffle • A Soggy Waffle
0 votes
1 reply
851 views
BWA align in human and parasite genome, and sort them
bwa
updated by GenoMax GenoMax • written by Bender • Bender
0 votes
3 replies
1.1K views
Use of "grep" in RNAseq trimming
rnaseq polya
updated by GenoMax GenoMax • written by Luna_1215 • Luna_1215
0 votes
1 reply
813 views
No change in quality score graph even after adapter removal
rna-seq fastqc trimmomatic
updated by dsull dsull • written by Luna • Luna
2 votes
1 reply
957 views
Regarding ClinVar's VCF file
matrix disease vcf clinvar gene
updated by Jeremy Leipzig Jeremy Leipzig • written by singhankit973 • singhankit973
0 votes
10 replies
2.4K views
Single-cell dimensionality reduction and clustering
seurat
updated by ATpoint ATpoint • written by xingyu • xingyu
0 votes
0 replies
623 views
How to load series matrix file into SeSAMe or minfi for processing?
sesame geo illumina minfi machine-learning
updated by Ram Ram • written by Junk • Junk
0 votes
14 replies
7.3K views
Is there anyone who downloaded Azimuth packges?
azimuth scrnaseq
updated by ATpoint ATpoint • written by kayah • kayah
0 votes
10 replies
2.6K views
Error in conversion of ensembl to gene names
ensembl biomart
updated by Istvan Albert Istvan Albert • written by anasjamshed anasjamshed
1 vote
1 reply
1.1K views
Tool: CellLocator: An Open-Source Tool for Unlocking Deeper Insights from Live-Cell Imaging
open-source deep-learning denoising single-cell incucyte
written by Michael • Michael
0 votes
5 replies
1.7K views
Which data to choose for correlation examination
correlation wgcna tpm batch spearman
updated by Zhenyu Zhang Zhenyu Zhang • written by lyan125 • lyan125
0 votes
12 replies
2.9K views
Transcript coverage 3' bias. Is it really that determining?
mappings transcriptome rna
updated by i.sudbery i.sudbery • written by Amb@r85 • Amb@r85
0 votes
7 replies
1.9K views
Quantify miRNAs from whole transcriptome library (single end, TruSeq, 100bp)
mirna whole-transcriptome-truseq
updated by Ram Ram • written by w.denhollander • w.denhollander
0 votes
1 reply
1.1K views
comparing STARsolo UMI-based directional deduplication vs umi-tools?
single-cell starsolo deduplication umi-tools
updated by i.sudbery i.sudbery • written by mk mk
0 votes
0 replies
561 views
Prediction of sRNA in FASTA file
fasta prediction srna
written by nashwaabdulrasheed09 • nashwaabdulrasheed09
0 votes
0 replies
550 views
Identification of SSR markers from RNA-seq data
misa ssr-markers data rna-seq
written by Kutti • Kutti
0 votes
9 replies
2.9K views
Super enhancer calling using ROSE for mm39 genome: list index out of range error
chip-seq super-enhancers rose mm39
written by Gayatri • Gayatri
0 votes
1 reply
863 views
assembling human mitochondrial genomes with nanopore long reads
ont assembly genome mitochondria nanopore
written by eebloom • eebloom
2 votes
12 replies
9.1K views
how can i download human ribosomal reference ?
rna-seq rrna
updated by tomas4482 • tomas4482 • written by sabaghianamir70 • sabaghianamir70
0 votes
4 replies
1.4K views
How should the order of microbiome data preprocessing be prioritized?
aggregation microbiome preprocess normalization filter
written by ssko • ssko
0 votes
10 replies
3.6K views
High Detection of Duplication in RNAseq dataset
deduplication rnaseq
updated by i.sudbery i.sudbery • written by karlensberg • karlensberg
0 votes
6 replies
2.5K views
What should I do if death cell counts and types biologically important in my single cell data?
scrna cell-death single-cell
updated by i.sudbery i.sudbery • written by carolofharvest • carolofharvest
0 votes
1 reply
1.8K views
Salmon low mapping rates
reference mapping salmon rna-seq
updated by jnechacov • jnechacov • written by L.Chang • L.Chang
0 votes
3 replies
1.7K views
Removing gDNA contamination from RNA seq data
contamination gdna
updated by i.sudbery i.sudbery • written by yahav.bracha • yahav.bracha
0 votes
2 replies
1.3K views
dorado and modkit for m6A identification
dorado m6a modkit
written by baibhu1234 • baibhu1234
0 votes
0 replies
482 views
cnvkit results with start positions always 0 ?
cnvkit variant-calling
updated by Ram Ram • written by ank • ank
0 votes
0 replies
988 views
Regression and scaling in scanpy
scanpy
written by bioinfo • bioinfo
0 votes
2 replies
1.0K views
Question about metabolic pathway prediction using only DNA sequencing data
metabolism genomics ngs
updated by hakimbazol • hakimbazol • written by Mark • Mark
0 votes
6 replies
1.7K views
English terms distinguishing genotype allelic nucleotides (T/C) from VCF encoded genotype (0/1)
genotypes vcf
written by Jeremy Leipzig Jeremy Leipzig
0 votes
0 replies
823 views
How to define a clonotype by its TCR sequencing data with its own structure.
tcr sequencing clonotype scrna
written by diqixiaoyaoer • diqixiaoyaoer
0 votes
2 replies
1.3K views
Getting fasta sequence for a gene
fasta regulatory genome region gene
updated by Istvan Albert Istvan Albert • written by zizigolu zizigolu
0 votes
3 replies
1.3K views
Identification of variants from Spatial Transcriptomics using STARSolo
spatial-transcriptomics star visium
updated by Ram Ram • written by kanika.151 kanika.151
0 votes
6 replies
2.6K views
Seurat Mito Prefix Removed from Features
seurat
updated by yura.grabovska • yura.grabovska • written by Koki • Koki
0 votes
1 reply
1.1K views
Is there a way to write a genbank file in R?
r genbank genetics bioconductor
updated by yura.grabovska • yura.grabovska • written by Jack • Jack
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