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121,961 results • Page 180 of 2440
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After merging batches, I got very segmented umap in scanpy
scanpy single-cell
22 months ago by MohammadAlkadi ▴ 70
0
votes
0
replies
512
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq deseq2
22 months ago by pl23 • 0
2
votes
12
replies
2.9k
views
BCL2FASTQ: Segmentation Fault Error (segfault)
linux Segmentation-fault bcl2fastq
22 months ago by gillhuberfelix ▴ 20
8
votes
5
replies
9.4k
views
6 follow
Mitochondrial genes in single cell nuclear RNAseq data
RNA-Seq gene mitochondria
updated 22 months ago by ★ 2.7k • written 6.7 years ago by ▴ 60
0
votes
2
replies
1.0k
views
Find Genes in Homer Analysis that have the enriched Motif
single ORA nucleus mRNA Homer
22 months ago by je71xusa • 0
0
votes
2
replies
925
views
Tool to get genes in the neighbourhood of a particular gene
locus Gene
updated 22 months ago by ★ 1.5k • written 22 months ago by ▴ 90
0
votes
0
replies
539
views
News: GWAS course
R GWAS
updated 22 months ago by 45k • written 22 months ago by ★ 2.6k
3
votes
3
replies
1.9k
views
Salmon index problem
Salmon docker RNAseq index refgenie
updated 22 months ago by ★ 1.5k • written 22 months ago by ▴ 20
2
votes
3
replies
1.2k
views
BWA mem align reads with MQ = 0 to only one region (reference genome has two similar sequences).
NGS BWA
updated 22 months ago by ★ 1.5k • written 22 months ago by ▴ 20
2
votes
2
replies
1.5k
views
Merging several vcf files for GWAS?
R beginner gwas ngs novogene
22 months ago by sabrilo171 ▴ 20
7
votes
5
replies
2.5k
views
bcftools error: : error while loading shared libraries: libcrypto.so.1.0.0:
bcftools
22 months ago by jiyoung ▴ 20
2
votes
9
replies
2.8k
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR Salmon mapper aligner RNAseq
22 months ago by ian.will ▴ 30
2
votes
2
replies
2.2k
views
Help with scvelo
scvelo
updated 22 months ago by ★ 2.7k • written 23 months ago by ▴ 360
1
vote
9
replies
4.8k
views
PCAtools data file not linking to metadata file
R PCA RNA-Seq PCAtools
updated 22 months ago by 89k • written 5.3 years ago by ▴ 10
1
vote
0
replies
1.1k
views
Job: Fully funded PhD positions, Vienna, Austria
fully-funded phd
updated 22 months ago by 8.0k • written 22 months ago by ▴ 10
0
votes
2
replies
1.8k
views
Use of IDR after running MACS3 for ATAC-seq data
ATAC-seq MACS2 MACS3
22 months ago by Orange ▴ 30
2
votes
2
replies
1.0k
views
how do I assemble centromere regions in a plant genome?
novo de assembly
updated 22 months ago by 48k • written 22 months ago by • 0
4
votes
9
replies
1.9k
views
Working with NCBI downloadable Datasets
NCBI Genedata Datasets
updated 22 months ago by ★ 1.6k • written 22 months ago by • 0
1
vote
2
replies
908
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole genome assembly sequencing
updated 22 months ago by 48k • written 22 months ago by ▴ 60
9
votes
9
replies
2.4k
views
How to filter .fasta file based on conditional statement
abundance filtering fasta vsearch
22 months ago by rDNA ▴ 20
1
vote
3
replies
1.1k
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R complexheatmap
updated 22 months ago by ★ 1.9k • written 22 months ago by ▴ 10
0
votes
0
replies
573
views
Find equivalent pathways between KEGG, Reactome, and WikiPathways
pathway mapping database
22 months ago by Ngrin • 0
0
votes
0
replies
442
views
GenAlEx Haploid Data Detecting Recombination
GenAlEx Popgen Haploid Recombination
22 months ago by turcoa1 • 0
4
votes
2
replies
1.2k
views
What is Bowtie2 --norc parameter?
bowtie2 norc alignment
21 months ago by lvl2111 • 0
2
votes
1
reply
768
views
Shorten Illumina reads
RepeatExplorer2 Illumina paired-end
updated 22 months ago by 20k • written 22 months ago by ▴ 40
0
votes
2
replies
838
views
Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA
translation Variant proteomics FASTA VCF
22 months ago by chscho • 0
0
votes
1
reply
610
views
miRNA annotation miRge3.0
miRge3
updated 22 months ago by ★ 1.9k • written 22 months ago by ▴ 60
0
votes
0
replies
538
views
cNMF vs LIGER
NMF correction batch
22 months ago by e.r.zakiev ▴ 260
1
vote
4
replies
986
views
Analyze with Geo2R
R NCBI
22 months ago by anasjamshed ▴ 140
1
vote
3
replies
1.5k
views
did pilon improve my genome?
genome genomeassemblies assembly spades pilon
updated 22 months ago by ▴ 660 • written 22 months ago by • 0
2
votes
7
replies
18k
views
How too choose outgroup for rooting a phylogenetic tree?
phylogeny sequence alignment
updated 22 months ago by ▴ 80 • written 10.5 years ago by ★ 2.8k
2
votes
3
replies
1.5k
views
Regarding using a "pseudo reference genome" for aligning short reads
genomics
20 months ago by pixie@bioinfo ★ 1.5k
6
votes
3
replies
1.1k
views
BBDuk error: with these 4 lines....
BBDUK trimming java
22 months ago by blackadder ▴ 30
0
votes
0
replies
1.4k
views
For people doing high molecular weight DNA sequencing library prep, do you see a steep drop off in the fragment sizes before and after the library pr…
library-prep sequencing ont nanopore ngs
22 months ago by Mark ▴ 60
0
votes
0
replies
899
views
Creating heatmap for ChIP-seq using deeptools
heatmap chipseq chip deeptools visualization
22 months ago by biology_inform ▴ 60
6
votes
6
replies
1.7k
views
6 follow
How to align a genome fasta file from NCBI to a reference genome?
genome genetics alignment
updated 22 months ago by ★ 5.2k • written 22 months ago by • 0
0
votes
7
replies
1.3k
views
snp database using annotation
database gwas snp annotation
22 months ago by sskimvd • 0
0
votes
1
reply
630
views
error in plink
plink prs polygenic-risk-score
updated 15 months ago by 45k • written 22 months ago by • 0
0
votes
2
replies
1.1k
views
how to use pilon
genome pipelines assembly pilon contig
updated 22 months ago by 3.4k • written 22 months ago by • 0
3
votes
2
replies
774
views
t-test by row
R t-test
updated 22 months ago by ★ 3.1k • written 22 months ago by ▴ 20
0
votes
0
replies
485
views
jellyfish histo is empty
jellyfish kmer fastq
22 months ago by m.t.lorenc • 0
1
vote
8
replies
2.4k
views
AVX error with Deepvariant caller
VCF variant-caller deepvariant
updated 22 months ago by 20k • written 22 months ago by ▴ 20
0
votes
2
replies
937
views
What is the best way to identify which group of genes is more highly expressed?
R gene-expression rna-seq
22 months ago by pl23 • 0
3
votes
0
replies
854
views
News: NCBI BLAST+ 2.2.15 now available for download
NCBI Taxonomy BLAST
22 months ago by PeterC_NCBI ▴ 520
0
votes
1
reply
835
views
update FMT/GT in VCF file using bcftools annotate
bcftools annotate VCF
updated 22 months ago by 166k • written 22 months ago by • 0
5
votes
3
replies
3.8k
views
How to overlap patient VCF with ClinVar database annotation using bedtools?
bedtools bash ClinVar overlap VCF
updated 22 months ago by 45k • written 22 months ago by ▴ 10
0
votes
0
replies
517
views
Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject
giraffe surject vg
22 months ago by cassiwatt ▴ 10
1
vote
2
replies
1.0k
views
How to identify the nearest gene associated with a specific SNPs?
RSID GWAS
updated 22 months ago by ▴ 930 • written 22 months ago by ▴ 160
13
votes
6
replies
1.6k
views
6 follow
how to sort fasta file according to a header file
fasta
updated 22 months ago by 45k • written 22 months ago by ▴ 20
7
votes
4
replies
1.8k
views
NCBI Eutils error forwarding request
eutils pubmed
updated 22 months ago by 45k • written 22 months ago by ▴ 30
121,961 results • Page 180 of 2440
Recent Votes
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
Answer: Gene Ontology visualization
A: For CreateSeuratObject, Where Do the Values for min.cells and min.features come
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
Answer: With 10x Visum HD : How to map the barcode id to the barcode sequence ?
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Answer: Differences between published differential gene expression results and own analy by yura.grabovska ▴ 820
When you say vastly different, what do you mean exactly? Does your top 100 up/down not match theirs at all?
Comment: Functional prediction for proteins of bacteria. by colindaven 8.0k
Have a look at tools like SnpEff or Ensembl VEP. Perhaps your bacterial sp is included.
Comment: Errors with RSEM/bowtie2 by Olivia • 0
Yes, I already made the transcriptome with these tools, and the CD-HIT-EST fasta file is the transcript file that I am using for RSEM. Then…
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks by Guilherme • 0
Oh, ok. It seems like NCBI stores the files in SRA format (thus needing conversion and database lookups by sra toolkit tools) and EBI store…
Comment: help with modkit on nanopore sequencing data. by andres.firrincieli 3.9k
On the DMR tutorial page, they retrieve Human CpG Islands from the UCSC Table Browser. You can do the same thing for Mouse CpG Islands. Hav…
Comment: After doublet detection in 10x scRNA-Seq data, there is still evidence of double by yura.grabovska ▴ 820
Yes but the problem is that biological knowledge is never fully encompasing. While I can say that a cell expressing CD45 alongside astrocyt…
Comment: DNA copy number blacklist for excluding common unreliable regions by yura.grabovska ▴ 820
Human genome, ideally hg38
Comment: Is Newbler still available for download by anweshaash • 0
Hello, I am wondering if you got access to the software or not. I am looking to use Newbler for my research and I contacted Roche too but t…
Comment: Errors with RSEM/bowtie2 by GenoMax 154k
> I have previously run Trinity with the Trimmomatic step as well as CD-HIT-EST. I assume you did the above to generate the transcriptome,…
Answer: With 10x Visum HD : How to map the barcode id to the barcode sequence ? by sacha ★ 2.5k
Got it https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-inclusion-list-formerly-barcode-whitelist
Comment: limmaFit error when comparing TCGA RNA-Seq data by vernonlim98 • 0
Thanks for the advice. Am still new to RNA seq and R programming in general, and will just do the analysis by myself.
Answer: The Biostar Handbook. A bioinformatics e-book for beginners. by Istvan Albert 103k
Update as of **August 2025**: The book now includes a new online course: [**FastTrack Bioinformatics 2025**][course] at no extra cost. Bio…
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks by GenoMax 154k
Likely because the SRA programs are doing database look ups as they retrieve the data where as with `curl` you are simply getting pre-exist…
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks by Guilherme • 0
That's a great tool! I wonder why downloading through curl via SRA's ftp is SO MUCH faster than through sra toolkit programs (fastq-dump or…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by GenoMax 154k
> they should align with common sequence at some ends, making one longer consensus sequence. You don't want to simulate reads like this.…
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