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121,907 results • Page 35 of 2439
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5
votes
3
replies
769
views
Extracting Sequences from a FASTA File Using Exon Coordinates from a GTF File
gtf fasta
updated 7 months ago by 7.9k • written 7 months ago by ▴ 20
0
votes
2
replies
487
views
Low Read Mapping for Differentially Expressed Genes in 3' RNA-seq Analysis
gene-expression single-end RNA-seq
updated 7 months ago by 45k • written 7 months ago by ▴ 20
2
votes
3
replies
748
views
mapDamage error
mapDamage 1000genomes
7 months ago by anna.utili • 0
0
votes
0
replies
423
views
News: Online Course: Flow Cytometry Data Analysis with R/Bioconductor (17–20 March 2025)
R Bioconductor Flow-Cytometry Cancer-Genomics
7 months ago by Physalia-courses ★ 2.6k
2
votes
1
reply
722
views
Average length of mRNA on NCBI annotation seems too high
mRNA
updated 7 months ago by 15k • written 7 months ago by • 0
0
votes
0
replies
352
views
How to normalize qPCR results for covariates like cell type markers
Normalization qPCR RNA-Seq
7 months ago by Sara ▴ 40
0
votes
4
replies
966
views
Proteomics Data Analysis
Proteomics
updated 7 months ago by 89k • written 7 months ago by • 0
0
votes
0
replies
387
views
Demultiplexing asymmetrically barcoded reads from multiplex amplicon nanopore sequencing
ONT demultiplex
7 months ago by michael.flower.14 ▴ 210
6
votes
8
replies
1.5k
views
Regex in umi-tools doesn't identify pattern in non-beginning positions
whitelist UMI-Tools UMI UMI-TOOLS umi-tools
updated 7 months ago by 22k • written 7 months ago by ▴ 10
1
vote
1
reply
612
views
GRCh38 reference paths in human pangenome
HPRC GRCh38
updated 7 months ago by ★ 4.3k • written 7 months ago by • 0
2
votes
1
reply
596
views
Annotate WGS VCF with Allele Frequencies
snpeff vcf wgs allele
updated 7 months ago by 166k • written 7 months ago by • 0
1
vote
4
replies
890
views
dentifying tumor vs normal cells in spatial transcriptomics
seurat xenium spatial-transcriptomics
7 months ago by geno89 ▴ 20
2
votes
2
replies
1.4k
views
Which zUMIs output to use for differential gene expression?
zumis rnaseq smartseq3 single-cell
updated 7 months ago by ★ 7.7k • written 2.1 years ago by ★ 1.7k
0
votes
1
reply
581
views
build a diploid reference using cactus-pangenome pipeline
cactus pangenome diploid graph vg
updated 7 months ago by ★ 2.9k • written 7 months ago by ▴ 10
1
vote
0
replies
582
views
VEP doesn't count CADD
CADD VEP annotation
7 months ago by balanannie ▴ 10
6
votes
9
replies
6.3k
views
6 follow
News: New in DiffBind: dba.plotProfile() - Peak profiles and profile heatmaps
DiffBind ChIP-seq deepTools visualization ATAC-seq
updated 7 months ago by ▴ 20 • written 4.3 years ago by ★ 2.1k
2
votes
1
reply
532
views
Per tile sequence fails after trimming
fastQC WES Sequencing
updated 7 months ago by 153k • written 7 months ago by ▴ 20
0
votes
0
replies
358
views
Pipelines/Tools for cleaning UK Biobank data?
UKBiobank RAP
7 months ago by Christian • 0
0
votes
0
replies
438
views
Key error when using prepDE.py
python prepDE stringtie keyerror
updated 7 months ago by 48k • written 7 months ago by • 0
0
votes
2
replies
761
views
Scdblfinder issue
R scdblfinder
updated 7 months ago by 45k • written 7 months ago by • 0
0
votes
0
replies
464
views
Repeat Modeler Database Generation
repeat_modeler repeats fungi annotation genomes
7 months ago by SomeOne ▴ 240
1
vote
3
replies
769
views
Proteomics DEA
Proteomics
updated 7 months ago by 89k • written 7 months ago by • 0
0
votes
0
replies
385
views
Difficulty Finding LRR SD and BAF Drift in GenomeStudio 2.0
array LRR BAF genomestudio snp
7 months ago by Josephine H. • 0
6
votes
5
replies
1.6k
views
ATAC-seq paired-end data peakcalling on MACS3 - BAMPE vs (BAM and shift with extsize)
MACS3 BAMPE BAM Peakcalling ATAC-seq
updated 7 months ago by 89k • written 7 months ago by ▴ 10
0
votes
1
reply
387
views
LH Sequencing Machine?
fastq
updated 7 months ago by 153k • written 7 months ago by • 0
7
votes
6
replies
977
views
6 follow
High memory sorting of kmers - best way to use sort
uniq linux sort kmers
updated 7 months ago by 36k • written 7 months ago by ▴ 30
0
votes
0
replies
373
views
News: Bayesian Data Analysis in R – Online Course (March 3-7)
R RegressionModeling Statistics Byesian
7 months ago by Physalia-courses ★ 2.6k
0
votes
0
replies
342
views
Age covariate in GWAS
GWAS
7 months ago by aaaniich • 0
7
votes
8
replies
1.4k
views
How well was the rRNA depletion for RNA-Seq experiments
contamination star rrna bbduk ribodetector
updated 7 months ago by 153k • written 7 months ago by ▴ 80
0
votes
0
replies
382
views
News: Introduction to Machine Learning with R - online, March 3–7
R Machine-Learning omics Genomics
updated 7 months ago by 45k • written 7 months ago by ★ 2.6k
0
votes
0
replies
1.2k
views
Job: 2025 Summer Internship Opportunity in Computational Biology
intern
7 months ago by Shicheng Guo ★ 9.6k
3
votes
5
replies
1.8k
views
Tools for fasterq file?
trimming
updated 7 months ago by ▴ 390 • written 2.9 years ago by ▴ 60
4
votes
9
replies
2.3k
views
How to convert fasterq File into fastq files ?
fastq fasterq
updated 7 months ago by ▴ 390 • written 2.8 years ago by ▴ 20
2
votes
5
replies
609
views
How to extract DEGs from GEO database
extract DEGs
7 months ago by harrydo1892 • 0
11
votes
5
replies
776
views
In silico prediction if a phage can invade a bacterium
phage bacterium
7 months ago by A_heath ▴ 170
0
votes
4
replies
4.0k
views
BEAST and BEAGLE installed using conda environment, how to connect?
BEAST BEAUTI
updated 7 months ago by • 0 • written 5.7 years ago by ▴ 90
4
votes
4
replies
876
views
Dimensionality reduction using RNA and protein expression
dimensionality-reduction RNA-seq spatial
7 months ago by noodlejackson ▴ 40
5
votes
2
replies
1.1k
views
java out of memory error through beagle for imputation
beagle imputation java
updated 7 months ago by 45k • written 16 months ago by ▴ 70
0
votes
2
replies
885
views
BioPython load/save from SnapGene
biopython
7 months ago by tada • 0
2
votes
1
reply
19k
views
Herald: The Biostar Herald for Monday, February 10, 2025
herald
updated 7 months ago by 6.5k • written 7 months ago by 3.6k
1
vote
1
reply
635
views
Get bond angles for nucleotides in pdb/cif structure file
cif cryoEM pymol pdb structure
updated 7 months ago by ★ 3.1k • written 7 months ago by ▴ 650
4
votes
7
replies
885
views
merging .fastq.gz files results in corrupted files
corrupt gzip
7 months ago by rDNA ▴ 20
1
vote
1
reply
470
views
Installing VEP for a Specific Chromosome (e.g., Chromosome 1) is not possible??
VEP
updated 7 months ago by ★ 3.1k • written 7 months ago by ▴ 50
0
votes
3
replies
706
views
Blast+ remote search for refseq reference genome
API refseq
updated 7 months ago by 153k • written 7 months ago by • 0
0
votes
1
reply
522
views
Finding target for the biologically active compound
target-prediction
updated 7 months ago by ★ 3.1k • written 7 months ago by • 0
0
votes
3
replies
788
views
single-cell transcriptomics and bulk proteomics data integration
integration omics data
updated 7 months ago by ▴ 390 • written 7 months ago by • 0
2
votes
3
replies
806
views
Split genotypes in VCF file
VCF genotype dipcall
7 months ago by Biomonika (Noolean) 3.2k
0
votes
2
replies
497
views
clinker, a gene cluster visualization tool, crashed its online site
cluster gene
updated 7 months ago by 89k • written 7 months ago by • 0
4
votes
2
replies
774
views
Using limma on a very low amount of genes
DE-Analysis limma
updated 7 months ago by 7.9k • written 7 months ago by ▴ 20
3
votes
2
replies
928
views
Snakemake version 8.27.1 on LSF cluster
metagenomics snakemake shotgun kraken2
updated 7 months ago by ▴ 530 • written 7 months ago by ▴ 10
121,907 results • Page 35 of 2439
Recent Votes
Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
Comment: Automatically annotating a feature using a genbank file
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
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Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
You could give `mapPacBio.sh` from BBMap suite a try while you wait for other answers. That works for reads up to 6 kb. BBMap has a new hom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
What is the average length of your reads? That error sounds like a bug, so you may want to post that on `STAR` repo as an issue. I assume …
Comment: Getting just fastqc.zip file? by pourhangleila95 • 0
I want to perform fastQC on my data.Do you use fastQC software for doing it?
Comment: Whole Genome Sequencing IG regions by 719 • 0
Sorry for the poor wording of the original post, also should say I really appreciate people taking a moment to look at my post. My main con…
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