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121,903 results • Page 30 of 2439
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0
votes
1
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420
views
Can DiffBind Perform Peak Calling and Differential Analysis Directly from BAM Files?
DiffBind CHIP-Seq
updated 6 months ago by 89k • written 6 months ago by ▴ 10
1
vote
6
replies
902
views
Dealing with UMIs
UMI
6 months ago by Ramon • 0
5
votes
4
replies
938
views
Does sam 2048 flag discriminate secondary from supplementary alignments?
samtools secondary supplementary alignment
updated 6 months ago by 153k • written 6 months ago by ▴ 40
0
votes
1
reply
822
views
monocle 3-- Could not get node in small cluster
monocle3
updated 6 months ago by ★ 2.7k • written 16 months ago by ▴ 120
0
votes
3
replies
657
views
How to extract CDS from WGS data in rice?
RAP-DB CDS Genomics WGS
updated 6 months ago by ★ 1.7k • written 6 months ago by ▴ 10
0
votes
0
replies
342
views
retrieve type translocation ,deletion, duplication with fusion RNA detection tools
fusions fusioncatcher arriba star
6 months ago by ieie ▴ 20
3
votes
2
replies
605
views
Block size of SSD file storage
snp assembly ssd
updated 6 months ago by 153k • written 6 months ago by ▴ 320
3
votes
2
replies
670
views
Impact of the number of PCs on the clustering in scRNA seq
clustering pca scrna-seq
updated 6 months ago by ★ 1.6k • written 6 months ago by ▴ 20
1
vote
2
replies
639
views
PLINK 1.07 Segmentation fault (core dumped)
PLINK
6 months ago by Alice • 0
0
votes
1
reply
543
views
Installing vg on Mac failed due to "Could not find libomp"
vg
updated 6 months ago by ▴ 820 • written 6 months ago by • 0
0
votes
0
replies
284
views
Integration of metabolomics and transcriptomic of
Metabolomics transcriptomics
6 months ago by somanin92 • 0
0
votes
0
replies
297
views
Semaglutide docked in Albumin PDB
sema Pdb semaglutide albumin
6 months ago by Hansen_869 ▴ 80
2
votes
3
replies
1.1k
views
Forum: Career Advice
careeradvice
updated 6 months ago by 5.9k • written 6 months ago by • 0
0
votes
1
reply
438
views
Manta <DUP:TANDEM> interpretation
structural
updated 6 months ago by 166k • written 6 months ago by ▴ 580
2
votes
5
replies
2.4k
views
How to completely align chromosomes/scaffolds from de novo genome assemblies using MUMMER or other tools?
visualization genome alignment
updated 6 months ago by ★ 2.9k • written 7 months ago by ▴ 10
0
votes
0
replies
266
views
Read length mismatch between bam and query reads
GMAP Pacbio
6 months ago by 蓝寒 • 0
0
votes
2
replies
433
views
blastp for short sequences not finding a sequence that I know is in the database
blastp short
6 months ago by ricfoz ▴ 100
0
votes
3
replies
716
views
cytoscape Stringdb identifiers can't be mapped to uniprot or ensembl
map stringdb cytoscape
updated 6 months ago by ▴ 310 • written 6 months ago by • 0
0
votes
2
replies
600
views
How to compute DS (diploid dosage) from HDS (haploid dosage) in VCF?
format question dosage hds
updated 6 months ago by 5.1k • written 6 months ago by • 0
2
votes
3
replies
758
views
How to assess differential gene expression over gradient of treatment levels with DESeq2?
DGE DESeq2
updated 5 weeks ago by 15k • written 6 months ago by ▴ 20
0
votes
1
reply
408
views
Filtering tidySummarizedExperiment by seqnames does not work as expected
tidySummarizedExperiment tidyomics plyranges GenomeInfoDb
6 months ago by Kateřina • 0
0
votes
2
replies
551
views
What statistical method would you use to compare individual microbiome samples?
comparison statistics microbiome
6 months ago by Bertalan_Takacs ▴ 140
0
votes
0
replies
391
views
Error: All provided root_pr_nodes must be present in the principal graph. error in monocle3
monocle3 scRNAseq
6 months ago by kayah ▴ 20
0
votes
0
replies
288
views
select a predefined number of gene sequences from a given dataset
polymorphism to sequences how
6 months ago by Gumindu • 0
0
votes
0
replies
338
views
Different counts of mapped bases between Samtools coverage and Qualimap bamqc
mapping samtools qualimap
6 months ago by pauline10albert • 0
0
votes
4
replies
566
views
Keep the sequencing depth info when mapping contigs in Minimap2
depth coverage minimap2
6 months ago by pauline10albert • 0
0
votes
0
replies
257
views
Variant Prioritization Tool for Mouse Transcriptome
mouse variant transcriptome prioritization
6 months ago by vireen105 • 0
2
votes
9
replies
1.6k
views
Find "phased segments" from trio VCF?
phased vcf genotyping variants phasing
6 months ago by cmdcolin ★ 4.3k
0
votes
1
reply
628
views
Fatal error while doing MD simulation in gromacs related to residuetypes.dat
error docking gromacs MD Molecular simulation
updated 6 months ago by ★ 30k • written 6 months ago by • 0
4
votes
5
replies
2.6k
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 6 months ago by ▴ 760 • written 20 months ago by ▴ 140
1
vote
0
replies
412
views
Conventions for designing flowcharts for bioinformatics workflows
workflow flowchart diagram pipeline
updated 6 months ago by 45k • written 6 months ago by ▴ 380
0
votes
4
replies
767
views
Difference in reads per cell between samples
seurat scrnaseq
6 months ago by taylor.pio • 0
0
votes
4
replies
682
views
variant calling and filtering
VCFTools Samtools BCFtools
updated 6 months ago by 15k • written 6 months ago by • 0
0
votes
0
replies
345
views
How best to classify consensus SVs merged from multiple callers
SV annotation variants nanopore WGS
6 months ago by eebloom ▴ 110
0
votes
2
replies
497
views
Annotation of long non-coding RNAs
long noncoding RNA
6 months ago by jain72744 ▴ 10
0
votes
0
replies
371
views
News: Online course: Assembly and Annotation of Genomes - March 17th-21st
Genome-Annotation Nanopore PacBio Illumina Genome-Assembly
6 months ago by Physalia-courses ★ 2.6k
4
votes
3
replies
680
views
suggestion for alternative splicing event detecting tools under two biological conditions
isoforms transcriptome
6 months ago by slin023 ▴ 20
0
votes
0
replies
404
views
Batch download AlphaFold structures
protein api python structure alphafold
6 months ago by Joe 22k
4
votes
2
replies
516
views
Help for building Pipeline for Modeller
modeller pipeline
updated 6 months ago by ★ 30k • written 6 months ago by • 0
0
votes
0
replies
339
views
News: Online Course – Flow Cytometry Data Analysis with R/Bioconductor (March 17-20)
R Bioconductor FlowCytometry
6 months ago by Physalia-courses ★ 2.6k
0
votes
2
replies
568
views
structural variation calling through delly is stuck at Split-read assembly step
short reads assembly
6 months ago by analyst ▴ 70
0
votes
5
replies
814
views
Variant calling in tumor/normal pairs is calling heterozygous positions
variant
updated 6 months ago by ★ 1.6k • written 6 months ago by ▴ 60
1
vote
10
replies
1.8k
views
How to create a command that matches 13 characters in each column to be extracted into a new file, and leave behind the unmatched ones
featureCounts
updated 6 months ago by 45k • written 6 months ago by • 0
1
vote
1
reply
809
views
Forum: Realistic expectations for the current job market?
career_advice resume job_market resume_advice employment
updated 6 months ago by 153k • written 6 months ago by ▴ 10
2
votes
3
replies
1.1k
views
Is there a way to download the embeddings of Evo2?
embeddings python evo2
updated 6 months ago by ★ 30k • written 6 months ago by ▴ 30
2
votes
1
reply
468
views
Bacterial genome visualization
plasmid bacteria genome gene
updated 6 months ago by 153k • written 6 months ago by ▴ 10
6
votes
12
replies
1.5k
views
Manual conversion of VCF genotypes to nucleotide sequence
vcf nucleotide sequence
updated 6 months ago by ★ 4.3k • written 6 months ago by ▴ 40
3
votes
1
reply
563
views
Current best practice for alignment and quantification for downstream analysis in DESeq2
R DESeq2 alignment
updated 6 months ago by 105k • written 6 months ago by ▴ 820
1
vote
4
replies
1.0k
views
STAR 2.7.11b FATAL ERROR could not open genome file genomeParameters.txt but it is not generated in this version
STAR
updated 6 months ago by 45k • written 6 months ago by ▴ 310
0
votes
0
replies
467
views
cytAssist manual alignment failing for visium HD and spaceranger count
spatial-transcriptomics visiumhd space-ranger
updated 6 months ago by 153k • written 6 months ago by ▴ 20
121,903 results • Page 30 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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