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0 votes
2 replies
1.2K views
identifying 3'utrs for multiple transcripts of genes from a summarized experiment.
biomart transcriptome utr
written by RNAseqer RNAseqer
0 votes
1 reply
961 views
ChIPSeeker not annotating with hg38, stuck on hg19
chipseeker atac-seq
updated by GenoMax GenoMax • written by John • John
0 votes
1 reply
769 views
I cannot obtain my counts in galaxy server
galaxy
updated by Ram Ram • written by Hossein • Hossein
0 votes
6 replies
1.6K views
Illumina HumanHT-12 V4.0 analysis but I only have the .IDAT files
illumina expression-analysis microarray
updated by Basti • Basti • written by isaac_mani • isaac_mani
1 vote
0 replies
771 views
edgeR questions for use with cytometry counts
edger cytometry diffcyt
written by SamGG • SamGG
0 votes
6 replies
2.2K views
Analyze read lengths in Illumina data
human illumina libraries
updated by Pierre Lindenbaum Pierre Lindenbaum • written by María José • María José
1 vote
3 replies
1.6K views
Convert Long Nanopore reads to Illumina Paired end reads
illumina sequencing reads nanopore
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Mark • Mark
0 votes
0 replies
425 views
(Too?) Simple Deep Mutational Sequencing pipeline for fastq to enrichment score
deep-mutational-sequencing enrichment-score
written by Flipstone • Flipstone
0 votes
1 reply
1.2K views
Seeking Public Nanopore Datasets (FAST5 + FASTA/FASTQ) for DNA Storage Research
nanopore-sequencing machine-learning fast5 dna
updated by Ram Ram • written by Dev • Dev
0 votes
3 replies
1.2K views
Umi_tools regex blank output
regex umi_tools
written by amyruthvandiver • amyruthvandiver
0 votes
0 replies
572 views
RAxML or BV-BRC tree
raxml tree phylogenic bv-brc
written by anna • anna
0 votes
0 replies
659 views
Choosing the better input files for COGclassifier tool
classifier cog
written by anna • anna
0 votes
0 replies
629 views
Anti-ligand , receptor blocking and cell cell interaction analysis
cellchat cell nichenet single
written by carolofharvest • carolofharvest
0 votes
0 replies
1.2K views
How can I linearize certain segments within an existing protein structure constraining to volumetric grids using PyMOL scripting?
python protein-structure structural-bioinformatics protein
written by Aman Vishwakarma • Aman Vishwakarma
0 votes
5 replies
1.8K views
Overlapping regions in bedGraph
bedgraphtobigwig bedgraph
updated by Ram Ram • written by Aayush • Aayush
1 vote
3 replies
2.8K views
How to estimate and visualize haplotype blocks on a phased VCF/BCF
haplotype vcf
updated by cmdcolin cmdcolin • written by William William
0 votes
3 replies
953 views
Low RIN, novel samples
rin rna
written by Emilie • Emilie
0 votes
7 replies
1.9K views
Why don't mRNA levels measure protein synthesis rates?
mrna translation protein-synthesis rnaseq
updated by Ram Ram • written by Qroid • Qroid
2 votes
9 replies
2.1K views
Drosophila melanogaster dm3 intron percentage too high
drosophila sequence nucleotide intron genomics
updated by Istvan Albert Istvan Albert • written by Christian • Christian
0 votes
3 replies
2.7K views
Finding high number of significant genes by FindMarkers by Seurat
findmarkers single-cell seurat
updated by jared.andrews07 jared.andrews07 • written by Rosa Icela • Rosa Icela
0 votes
3 replies
1.2K views
What is the next step after getting the raw counts matrix for RNA-seq data?
deseq2 transriptomics rna-seq
updated by Istvan Albert Istvan Albert • written by rajdeepboral00 • rajdeepboral00
0 votes
11 replies
4.4K views
How can I linearize certain residues within an existing protein structure to create a dumbbell-shaped structure?
pymol python biopython structural-bioinformatics
written by Aman Vishwakarma • Aman Vishwakarma
0 votes
1 reply
1.5K views
codon adaptation index (CAI) estimation
codon-usage
updated by Ram Ram • written by rthapa • rthapa
0 votes
3 replies
1.1K views
High adj. p-value/FDR despite large FC and high expression levels
edger deseq2 rna-seq
updated by yura.grabovska • yura.grabovska • written by nik.kraemer • nik.kraemer
0 votes
1 reply
697 views
Why Is My Uniquely Mapped Read Count Higher in Samtools Compared to Bowtie2?
bowtie2
updated by Istvan Albert Istvan Albert • written by daffodil • daffodil
0 votes
0 replies
343 views
XR-seq processing pipeline
xr-seq
written by sleepystudent • sleepystudent
0 votes
0 replies
490 views
Smart-Seq3 intron+exon meaning
exon r smart-seq3 plots intron
written by Evlampia • Evlampia
0 votes
0 replies
544 views
I'm not sure what is going on with my DEXSeq object
genomicranges dexseq help rna-seq summarizedexperiment
written by cftattersfield • cftattersfield
0 votes
1 reply
843 views
ChIP-seq signal across bed regions
normalisation chipseq quantification signal
updated by mark.ziemann mark.ziemann • written by sk_24 • sk_24
0 votes
2 replies
1.1K views
Reading location of a feature of a miRNA entry in miRBase in EMBL format
format mirbase embl
written by Coleman • Coleman
0 votes
3 replies
1.5K views
How can you interpret a phased VCF with no "phase set" field (PS)
variants vcf phasing genotyping
written by cmdcolin cmdcolin
0 votes
6 replies
2.1K views
How to make a .gaf file for GO analysis
ngs go
written by noodle noodle
0 votes
5 replies
1.5K views
bigWig size difference between variableStep and fixedStep wig files
bigwig wig
written by notthebmovieactor • notthebmovieactor
0 votes
6 replies
1.5K views
Unannotated reads through STAR
star igv unannotated-reads
written by rajdeepboral00 • rajdeepboral00
0 votes
2 replies
858 views
multiple outputfiles after bamtofastq for same library
cellranger 10x bamtofastq
updated by GenoMax GenoMax • written by Tolga • Tolga
0 votes
6 replies
1.4K views
Hisat2 index genome
hisat2
written by frarodmar17 • frarodmar17
9 votes
22 replies
66K views
Public Electronic Health Records Database
database
updated by Alex • Alex • written by Abhi Abhi
0 votes
1 reply
626 views
Comparison of metabolic data between groups (WT vs KO)
metabolism
updated by ATpoint ATpoint • written by solene.vardon • solene.vardon
0 votes
6 replies
1.7K views
Estimating mRNA Half-Life from Single Time Point Data Using mRNA/Ribo-seq Expression Data
regression mrna rna-seq ribo-seq
updated by Ram Ram • written by Ramya • Ramya
0 votes
0 replies
425 views
Random effect model RNAseq
rma metafor
written by a.stef.44 • a.stef.44
0 votes
3 replies
1.1K views
Barley, alignment rates
barley alignment-rate
written by IrK IrK
0 votes
0 replies
1.0K views
News: Introduction to Python for biologists course
ngs python programming
written by Physalia-courses Physalia-courses
5 votes
15 replies
45K views
Convert between RefSeq and Ensembl Transcript?
refseq ensembl
updated by GenoMax GenoMax • written by pwg46 pwg46
0 votes
5 replies
1.4K views
HELP with PacBio RS reads for epigenetics
pacbio bax.h5 rs
updated by Billy Rowell • Billy Rowell • written by sarajorqueraortega • sarajorqueraortega
0 votes
2 replies
1.1K views
Post-sequencing basecalling error in MinKNOW
minknow dorado long reads nanopore
written by Cedrick • Cedrick
0 votes
2 replies
777 views
why knocking down LEMD2 using siRNA gives handful DEGs?
knockdown sirna lemd2
written by goyal.shiwali • goyal.shiwali
0 votes
4 replies
2.1K views
'Model matrix not full rank'
deseq2 design matrix
updated by Santosh Anand Santosh Anand • written by Rish • Rish
0 votes
1 reply
960 views
Change threads (-T) in online Galaxy for featureCounts
featurecounts rna-seq threads galaxy
updated by GenoMax GenoMax • written by raeven.bastock • raeven.bastock
0 votes
1 reply
1.0K views
Process Illumina Sequencing Data.
human illumina libraries
updated by GenoMax GenoMax • written by María José • María José
1 vote
1 reply
825 views
vgconstruct crashes
vg
updated by anovak anovak • written by Uveyik • Uveyik
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