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121,959 results • Page 179 of 2440
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2
votes
2
replies
1.6k
views
Best practices for unstranded sequences in featureCounts
featurecounts overlapping unstranded
22 months ago by Enrique • 0
1
vote
1
reply
638
views
Choose between pvalue & pvalue.adj
volcanoplot
updated 22 months ago by 103k • written 22 months ago by • 0
0
votes
5
replies
1.4k
views
HTseq reports missing attribute name
htseq
updated 22 months ago by 103k • written 22 months ago by • 0
3
votes
0
replies
923
views
Herald: The Biostar Herald for Monday, November 27, 2023
herald
22 months ago by Biostar 3.6k
9
votes
15
replies
2.8k
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
22 months ago by analyst ▴ 70
4
votes
2
replies
2.6k
views
Masurca. Failed to pre-correct Nanopore data, please check your data!
Nanopore Masurca
updated 22 months ago by 8.0k • written 4.3 years ago by ▴ 100
0
votes
0
replies
475
views
Differentiate sequenced and imputed variants in BGEN files
imputation bgen ukb
22 months ago by user230613 ▴ 380
1
vote
4
replies
1.6k
views
Species coverage in the NCBI protein NR database ?
NR
updated 22 months ago by 103k • written 22 months ago by ▴ 10
0
votes
17
replies
2.8k
views
Issues while running htseq-count
Candida-glabrata RNA-seq htseq-count
21 months ago by Foad ▴ 10
0
votes
0
replies
400
views
addPatternDensity to qsea object
maxDensityPattern medip qsea
22 months ago by Jaykishan • 0
1
vote
1
reply
1.1k
views
Harmony integration PC variance explained
scRNA integration harmony
updated 22 months ago by ▴ 140 • written 22 months ago by • 0
0
votes
3
replies
888
views
merged rs number information
merged dbsnp
22 months ago by sskimvd • 0
2
votes
1
reply
884
views
Bedtools intersection
bedtools bed intersect vcf
updated 22 months ago by 166k • written 22 months ago by ▴ 10
0
votes
2
replies
877
views
RnBeads mean difference vs M-values
Methylation
updated 22 months ago by ★ 2.1k • written 22 months ago by ▴ 60
1
vote
2
replies
664
views
RnBeads which p-value to use
Methylation RnBeads
updated 22 months ago by 89k • written 22 months ago by ▴ 60
1
vote
1
reply
720
views
Beginner differential methylation analysis
Methylation
updated 22 months ago by ★ 2.1k • written 22 months ago by ▴ 60
4
votes
8
replies
3.6k
views
Docker: Pass reads file form host to container
docker
22 months ago by davidmaimoun ▴ 50
2
votes
1
reply
630
views
EnhancedVolcano underrepresenting DEGs
R
updated 22 months ago by 89k • written 22 months ago by ▴ 30
4
votes
5
replies
4.8k
views
PyMOL: Gaps in protein structure yet shown by the sequence
PyMOL structure protein
updated 22 months ago by ▴ 10 • written 2.6 years ago by ▴ 10
0
votes
0
replies
668
views
[maftools]Too many multi_hit and missense mutation
maftools gatk MAF data WES VCF
22 months ago by jiazheng_lin • 0
0
votes
1
reply
844
views
multiple condition and time course in RNA-seq
edgeR RNA-Seq DESeq2
updated 22 months ago by 22k • written 22 months ago by ▴ 30
0
votes
0
replies
595
views
Negative F statistics for sex check in plink
plink check sex
22 months ago by kl ▴ 20
2
votes
4
replies
1.5k
views
Should SMART-seq2 data be deduplicated in STAR?
SMART-seq2
22 months ago by anlinli.napert • 0
0
votes
3
replies
1.2k
views
Extracting list of identical items from several excel files
from excel items Extract file
updated 22 months ago by • 0 • written 22 months ago by ▴ 40
1
vote
3
replies
1.2k
views
Indexing by bowtie2 but aligning with STAR
STAR mm10 Bowtie2
updated 22 months ago by 45k • written 22 months ago by • 0
0
votes
1
reply
958
views
Chipseq peak calling and peak frequency region
chipseeker macs2
updated 22 months ago by 3.4k • written 22 months ago by ▴ 10
0
votes
3
replies
1.6k
views
subset a bam file
bam pysam NGS samtools
updated 22 months ago by 154k • written 22 months ago by • 0
1
vote
1
reply
914
views
Forum: want to work in open source project/project in bioinformatics
project
updated 22 months ago by 45k • written 22 months ago by • 0
0
votes
0
replies
837
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
22 months ago by rohitsatyam102 ▴ 940
2
votes
3
replies
1.9k
views
How to identify the 300 kb upstream and downstream genes of lncRNAs?
RNA-Seq lncRNA target genes upstream downstream
updated 22 months ago by • 0 • written 4.8 years ago by ▴ 80
4
votes
6
replies
2.0k
views
BLAST hits on viruses relate to different host than used
Phage BLAST Metagenomics
22 months ago by DonPhager • 0
0
votes
3
replies
1.2k
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA deconvolution Music Music2 bulk
updated 22 months ago by 89k • written 22 months ago by • 0
0
votes
3
replies
896
views
Annovar - Annotated file cells show string
annovar
22 months ago by Roshan • 0
2
votes
6
replies
2.1k
views
Genotypes in vcf files
genotypes vcf
updated 22 months ago by 23k • written 22 months ago by ▴ 250
1
vote
3
replies
1.4k
views
Genetic data QC prior to imputation
imputation
updated 22 months ago by ★ 1.5k • written 22 months ago by ▴ 20
4
votes
2
replies
903
views
Excel Pasting Question
Excel
updated 22 months ago by 166k • written 22 months ago by ▴ 10
2
votes
1
reply
1.9k
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW MinION Nanopore
updated 22 months ago by 154k • written 22 months ago by ▴ 50
0
votes
1
reply
721
views
htShinyExample-5.3 - not working
htShiny Oncoprint InteractiveComplexHeatmap
updated 22 months ago by 45k • written 22 months ago by ▴ 60
6
votes
5
replies
4.3k
views
Multi threading bowtie index
bowtie indexing
updated 22 months ago by 8.0k • written 10.1 years ago by ▴ 80
2
votes
4
replies
2.1k
views
Human mitochondrial reference genome
reference genome mitochondria
22 months ago by singhankit973 ▴ 20
1
vote
3
replies
1.1k
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
22 months ago by Sara ▴ 280
0
votes
0
replies
1.4k
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics telomeres reads
22 months ago by Mark ▴ 60
1
vote
3
replies
5.3k
views
DoubletFinder for Python?
scanpy doublets scrublet
updated 22 months ago by ★ 1.7k • written 2.7 years ago by ▴ 10
0
votes
0
replies
496
views
not best k value found
de assemblly assembly novo kmergenie
22 months ago by shaileshdesai76 • 0
7
votes
5
replies
3.1k
views
How to learn Scanpy
scanpy Python rna-seq
updated 22 months ago by ★ 2.7k • written 3.3 years ago by ▴ 30
5
votes
4
replies
1.5k
views
Is there a good software to generate test genomics data?
genomics testing benchmarking
updated 22 months ago by 20k • written 22 months ago by ▴ 60
3
votes
4
replies
1.4k
views
selection of reference genome
hg19 reference genome hg38
22 months ago by Tsin-Lau • 0
4
votes
5
replies
1.7k
views
Forum: Current Trends in Bioinformatics
structural-bioinformatics
updated 22 months ago by 45k • written 23 months ago by • 0
1
vote
1
reply
920
views
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
121,959 results • Page 179 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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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 ofarinas621 • 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.…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by cmdcolin ★ 4.3k
I believe the pairs will only have common sequence (e.g. the pairs will "overlap") if the insert size is small. the wgsim program has a fla…
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