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121,904 results • Page 32 of 2439
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votes
3
replies
637
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PCA for Batch effect
Batch WES PCA effect
updated 6 months ago by ★ 2.0k • written 6 months ago by • 0
2
votes
3
replies
709
views
Looking for an old-fashioned alignment editor
msa editor
updated 6 months ago by 153k • written 6 months ago by ▴ 10
0
votes
0
replies
349
views
eQTL mapping with imputed genotypes: use data from GT or DS slot of VCF?
eQTL VCF Imputation MatrixeQTL
6 months ago by Colari19 ▴ 90
2
votes
1
reply
540
views
Query on WES
WES
updated 6 months ago by 45k • written 6 months ago by • 0
0
votes
0
replies
419
views
Replace heterozygous genotypes with minor allele in a vcf file
genotype SNP vcf heterozygous
6 months ago by kumar.vinod81 ▴ 340
3
votes
4
replies
746
views
Enrichment analyses (GO TERM etc)
clusteprofiler somascan proteins enrichment
updated 6 months ago by ★ 2.0k • written 6 months ago by ▴ 20
1
vote
2
replies
585
views
Protoplast Transient Assay in Arabidposis
Transient-Assay Protoplast Arabidposis
updated 6 months ago by ★ 3.1k • written 6 months ago by • 0
3
votes
2
replies
1.1k
views
Plink removing a lot of samples
PLINK2 plink GWAS
6 months ago by Steven ▴ 50
9
votes
9
replies
1.6k
views
How to determine new bacterial species from custom isolate?
species genome submission
updated 6 months ago by ★ 4.0k • written 7 months ago by ▴ 760
0
votes
0
replies
307
views
The antibiotic resistome (args_oap, another bioinformatics tools)
resistome metagenome args_oap
updated 6 months ago by 45k • written 6 months ago by • 0
0
votes
0
replies
384
views
News: Gene Set Enrichment Analysis in R/Bioconductor course - Online, March 3-6. Last call
R Bioconductor Gene-Set-Enrichment-Analysis GSEA
updated 6 months ago by 45k • written 6 months ago by ★ 2.6k
1
vote
1
reply
503
views
Read depth for RNA-seq based Variant Calling
mouse read-depth rna-seq variant alignment
updated 6 months ago by 45k • written 6 months ago by • 0
0
votes
4
replies
4.6k
views
News: Web Scraping and Text Analysis in R (March 21st - April 11th, 2025) Course
rstats data-analysis web-scraping R
22 days ago by Transmitting Science communication ▴ 70
3
votes
2
replies
839
views
HaplotypeCaller Not Detecting Variants
GATK Variant-calling WGS
updated 6 months ago by 45k • written 7 months ago by ▴ 10
2
votes
3
replies
961
views
NCBI genome submission validation error
genome annotation
updated 6 months ago by 15k • written 6 months ago by ▴ 20
1
vote
1
reply
441
views
Infer amino acid alignment from pairwise nucleotide alignment
alignment
updated 6 months ago by ★ 1.6k • written 6 months ago by • 0
2
votes
1
reply
540
views
Query Regarding Missing Sample Paths in Graph-Based Pangenome Construction
variant-calling pangenome giraffe vg haplotypes
updated 6 months ago by 45k • written 6 months ago by ▴ 10
4
votes
4
replies
982
views
Variant Missing in VCF but Present in BAM Files: Discrepancy Identified via IGV Report in Join-Call Project
GATK Deepvariant BWA
updated 6 months ago by 166k • written 6 months ago by ▴ 20
2
votes
2
replies
529
views
Potential mapping issues in Cas9 knockout cells with STAR (the truncated RNA)
STAR RNA-seq
6 months ago by Weize ▴ 10
0
votes
3
replies
633
views
Normalizing Peaks in ChIP seq
ChIP-seq
updated 6 months ago by 45k • written 6 months ago by ▴ 170
1
vote
0
replies
393
views
Minimal Quality Control Thresholds in Shotgun or Amplicon Metagenomics for non assembly based analysis
QC Microbiome fastp
6 months ago by Maxwell ▴ 70
0
votes
0
replies
219
views
Estimating the Relative Abundance of a Species in a Mixed Microbial Community Using 16S PCR
16S
6 months ago by ljrdain2508 • 0
3
votes
2
replies
640
views
Training Augustus for Gene Prediction
Augustus Busco genome prediction gene
updated 6 months ago by ★ 2.4k • written 6 months ago by ▴ 10
0
votes
1
reply
463
views
Mus musculus genome scaffold discrepancy
genome ncbi
updated 6 months ago by ★ 2.1k • written 6 months ago by • 0
0
votes
1
reply
337
views
Edit Dataset FASTQ files using ReadStore Command Line Interface
FASTQ Readstore CLI
updated 6 months ago by 89k • written 6 months ago by • 0
0
votes
0
replies
226
views
plyranges – joining gpos object only by the start coordinate of the range
GenomicRanges plyranges
updated 6 months ago by 166k • written 6 months ago by • 0
0
votes
1
reply
400
views
Fast querying of variant metrics with database
python database
updated 6 months ago by 166k • written 6 months ago by ▴ 530
2
votes
2
replies
595
views
Mitochondrial Variant Calling Tools
Mitochondrial NGS Variant Calling Illumina
6 months ago by adarsh ▴ 60
1
vote
3
replies
3.5k
views
How to use harmony with scanpy?
scanpy harmony
updated 6 months ago by • 0 • written 7 months ago by ▴ 160
1
vote
2
replies
692
views
SpliceAI custom gene annotation file
GENCODE SpliceAI
6 months ago by ClkElf ▴ 50
1
vote
0
replies
801
views
Job: Postdoc in Reproductive genetics - bioinformatics
Sweden bioinformatics genetics postdoc
6 months ago by pol.sole.navais ▴ 10
0
votes
0
replies
623
views
What is a recommended maximum read depth threshold for DNA variant filtration, supported by scientific articles?
filtering articles-search read-depth variant-calling
6 months ago by Sofya • 0
9
votes
13
replies
3.1k
views
How are probabilities of insertions and deletions encoded in FASTQ?
fastq phred quality score nanopore pacbio indels
updated 6 months ago by 23k • written 6.6 years ago by ★ 1.8k
0
votes
2
replies
506
views
samtools mpileup and samtools tview give different reads quality results
samtools tview mpileup
6 months ago by cocoboxt • 0
9
votes
12
replies
8.3k
views
picard installation failure
error software picard
updated 6 months ago by 15k • written 8.0 years ago by • 0
1
vote
3
replies
690
views
low alignment rate for RNA-Seq data
rice low alignment RNA-Seq
updated 6 months ago by 153k • written 6 months ago by ▴ 70
3
votes
2
replies
542
views
Optimal Computer Configuration for Bioinformatics Analysis
scRNA-seq computer
6 months ago by Song ▴ 10
0
votes
0
replies
309
views
Anndata vs cloupe
seurat cloupe scanpy anndata
6 months ago by Rika • 0
0
votes
3
replies
636
views
Gene Mapping Issue
DAVID
updated 6 months ago by 15k • written 6 months ago by • 0
0
votes
0
replies
823
views
Job: Assistant, Associate, or Full Project Scientist in Molecular Biology
molecular teaching biology
6 months ago by UCSDBioSci ▴ 30
2
votes
4
replies
786
views
RNA variant calling - SNP and indels files
mouse variant_calling genomics RNA
6 months ago by littlebioinformatician • 0
5
votes
4
replies
769
views
Manta analysis in WES
Deletion MANTA WES SV Exomiser
6 months ago by Eduardo ▴ 20
0
votes
1
reply
290
views
All VS All contamination check for tumor samples
tumor contamination
6 months ago by mps • 0
1
vote
2
replies
412
views
Determine binding sites in unstimulated TF ChIP-seq samples
ChIP-seq csaw
6 months ago by Jacek ▴ 20
0
votes
1
reply
400
views
GO analysis custom reference?
GO-analysis
updated 6 months ago by ★ 3.1k • written 6 months ago by • 0
0
votes
2
replies
429
views
Query on WES
WES
6 months ago by rauf.sania786 • 0
0
votes
0
replies
334
views
News: Introduction to Machine Learning in R online course
R statistics AI machine-learning
updated 6 months ago by 45k • written 6 months ago by ▴ 70
6
votes
7
replies
2.2k
views
6 follow
Nanopore long-read sequencing doubts and problems
minmap2 long-reads NanoPlot Nanopore
updated 3 months ago by 7.9k • written 6 months ago by ▴ 10
1
vote
3
replies
711
views
cannot install GO.db in windows
GO.db
updated 6 months ago by 22k • written 6 months ago by • 0
1
vote
5
replies
1.1k
views
conda :FileNotFoundError: [Errno 2] No such file or directory
conda
updated 6 months ago by ★ 30k • written 6 months ago by • 0
121,904 results • Page 32 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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Recent Replies
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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