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121,908 results • Page 688 of 2439
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2.2k
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What is the difference between breakends and breakpoints?
aligner genomics
updated 4.5 years ago by ▴ 290 • written 4.5 years ago by ▴ 30
4
votes
6
replies
1.7k
views
I want to reverse the fasta sequence
fasta
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 40
1
vote
3
replies
1.6k
views
Finding ORFs from RNA-seq Sequence Data of eukaryotic species
nucleotide rna dna genome
updated 4.5 years ago by ★ 2.9k • written 4.5 years ago by ▴ 10
0
votes
1
reply
1.0k
views
genotype matrix
structure python
updated 4.5 years ago by ▴ 290 • written 4.5 years ago by • 0
1
vote
0
replies
916
views
xpEHH
genomics test snp
4.5 years ago by dominik.lagler ▴ 30
4
votes
1
reply
1.3k
views
Are alternative splicing analysis and differential expression analysis of RNA-seq data both needed?
rna
updated 4.5 years ago by ▴ 300 • written 4.5 years ago by • 0
3
votes
3
replies
2.1k
views
GWAS Summary statistic
gwas
4.5 years ago by Kevin • 0
4
votes
6
replies
2.1k
views
best method for splicing variant analysis if I have the counts already?
Bioconductor RNA-seq splicinganalysis isoform
4.5 years ago by decppced • 0
1
vote
1
reply
2.8k
views
hypergeometric test for under-representation/over-representation of cells in a cluster (scRNA-seq) (in R)
rna test
updated 4.5 years ago by 13k • written 4.5 years ago by • 0
2
votes
4
replies
5.5k
views
i have proteomics data in .raw format
protein
updated 4.5 years ago by ▴ 940 • written 4.5 years ago by ▴ 30
0
votes
2
replies
1.1k
views
Concatenating fastq files for better assembly
genomics assembly sequencing RNA-Seq
4.5 years ago by shail.nair05 ▴ 20
0
votes
0
replies
683
views
copy number variation analysis
gisticfile copynumberalteration
4.5 years ago by Rob ▴ 180
0
votes
0
replies
600
views
Is there any way to fix this biplot so all the ids are able to be seen?
fasta R
4.5 years ago by trejomarco6 • 0
1
vote
1
reply
3.1k
views
Plink extract missing (and replaced) variant IDs from VCF
plink
updated 4.5 years ago by 11k • written 4.5 years ago by • 0
0
votes
1
reply
867
views
Question about the DbSNP reference vcfs
mapping dna
updated 4.5 years ago by ▴ 290 • written 4.5 years ago by ▴ 10
5
votes
2
replies
1.2k
views
Heirarchal regression for model comparison, RNA-seq
R RNA-seq heirarchalregression
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 280
3
votes
3
replies
2.1k
views
Create a seurat object from a DESeqDataSet
Seurat R DESeq2
updated 4.5 years ago by ★ 19k • written 4.5 years ago by ▴ 70
0
votes
0
replies
665
views
Motif analysis from the Binding and expression target analysis (BETA) software
workflow motif
4.5 years ago by mwong043 • 0
0
votes
0
replies
782
views
Gene enrichment analysis - How to get the gene names in Entrez id's?
Bioconductor Geneenrichment RNAseq genomics
updated 4.5 years ago by 166k • written 4.5 years ago by • 0
1
vote
4
replies
1.4k
views
Does 5' read trimming affect duplicate detection?
NGS
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 20
4
votes
2
replies
2.3k
views
Extracting specific cancer types from MAF (Mutation Annotation Format) files from TCGA(The Cancer Genome Atlas)
ENCODE mutation maf TCGA cancer
4.5 years ago by peter ▴ 20
0
votes
1
reply
1.0k
views
how to run FATHMM-MKL program based on hg38?
FATHMM-MKL
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 100
14
votes
26
replies
17k
views
10 follow
makeblastdb Fasta file with 25 sequences gives Error: mdb_env_open: There is not enough space on the disk
blast makeblastdb
updated 4.5 years ago by ▴ 50 • written 5.8 years ago by ▴ 20
0
votes
0
replies
1.6k
views
Job: 2 Computational Biologist / Data scientist positions in single-cell and multi-OMICs data integration at Institut Imagine (Paris, FR)
single-cell sequencing genomics
updated 2.5 years ago by 45k • written 4.5 years ago by ★ 1.7k
2
votes
2
replies
3.4k
views
Question regarding TCGA and TCGAbiolinks --> RNAseq data as HTseq-Counts, FPKM, FPKM-UQ
RNAseq FPKM-UQ FPKM TCGAbiolinks TCGA
4.5 years ago by mario.red8976 ▴ 140
1
vote
1
reply
2.3k
views
Designing linear model matrix (limma) for differential methylation analysis using Illumina EPIC Methylation Array
EPICarray microarray DifferentialMethylation
updated 4.5 years ago by ★ 2.1k • written 4.5 years ago by • 0
0
votes
6
replies
1.9k
views
How do I filter interactions that are more than 100kb and less than 3kb
bed rna genome programming genomics
4.5 years ago by koushikayaluri ▴ 70
3
votes
6
replies
1.9k
views
Selecting genotypes for a specific chromosome belonging to a specific patient from a multi patient VCF file
sequence
4.5 years ago by dk0319 ▴ 70
0
votes
1
reply
868
views
Forum: Apache Spark on AWS
apachespark
updated 4.5 years ago by 23k • written 4.5 years ago by ★ 1.4k
0
votes
8
replies
3.1k
views
MACS: peak calling from snATAC data
ATAC MACS Rstudio Peakcalling
4.5 years ago by abiuma ▴ 30
0
votes
0
replies
777
views
Best way for finding annotated counterparts of unknown transcript after BLAST
blast efetch pipeline annotation
4.5 years ago by Mathias • 0
0
votes
0
replies
3.0k
views
MEGA X (but not MEGA 7) Error: Access Violation loading fasta file
MEGAXError:AccessViolationloadingfastafile
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
2
votes
1
reply
1.4k
views
Bedmethyl
methylation bedmethyl
updated 3.4 years ago by ▴ 120 • written 4.5 years ago by ▴ 50
12
votes
6
replies
11k
views
What do these MA plots signify?
seq rna maplot sequencing deseq2
updated 4.5 years ago by ▴ 170 • written 4.5 years ago by ▴ 10
3
votes
5
replies
2.2k
views
Is there a software for genomic calculation of GC content and Gene density under sliding windows?
GCcontent genedensity
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 20
1
vote
0
replies
1.3k
views
Combine multiple groups on comparison by edgeR
glm rna-seq edgeR
4.5 years ago by camelest ▴ 50
0
votes
0
replies
643
views
Unable to get root element from XML file
blast galaxy annotation
4.5 years ago by Pamela • 0
7
votes
4
replies
2.6k
views
Per base sequence content of FastQC Report
rna-seq
4.5 years ago by yueli7 ▴ 250
3
votes
3
replies
3.0k
views
How can I get the Shannon and observed alpha diversity Index value?
R
4.5 years ago by dpc ▴ 250
2
votes
5
replies
3.4k
views
Generating a heatmap in DEG analysis
Differential-gene-expression RNA-Seq
updated 17 months ago by 45k • written 4.5 years ago by ▴ 10
0
votes
2
replies
1.4k
views
How can a duplicate read be interchromosomal?
interchromosomal duplicate NGS samtools picard
4.5 years ago by maxrwjones ▴ 60
2
votes
3
replies
4.0k
views
ComplexHeatmap log scale gradient
log colours complexHeatmap
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
6
votes
9
replies
2.7k
views
what can i use many RNAseq data to do ?
RNA-Seq
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 10
2
votes
4
replies
1.7k
views
bidirectional blast p
Ensembl BLASTpbidirectional orthologus
updated 4.3 years ago by 45k • written 4.5 years ago by • 0
3
votes
2
replies
2.9k
views
UMAP of 10X and SmartSeq2 datasets on same plot
smartseq2 singlecellrna-seq umap 10xgenomics
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 350
0
votes
1
reply
760
views
Genes IDs of RNA_Seq results
gene format genome fasta conversion
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
0
votes
0
replies
498
views
Figure for relative error with large database
python database
4.5 years ago by Evy_00 • 0
1
vote
0
replies
1.6k
views
Job: Scientific Coordinator / Knowledge Graph Engineer
rdf sparql
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 760
0
votes
5
replies
2.6k
views
How to quickly find the position of k-mer on the genome
alignment sequencing k-mer
updated 3.4 years ago by • 0 • written 4.5 years ago by • 0
4
votes
5
replies
2.8k
views
Bowtie2 & Hisat2 SAM flags above 256?
manual SAM read-mapping flags bowtie2
4.5 years ago by maxrwjones ▴ 60
121,908 results • Page 688 of 2439
Recent Votes
Tried building a compact sequence format with 4-bit storage
Comment: Tried building a compact sequence format with 4-bit storage
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
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Recent Replies
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
I see, but the reason I was planning on using a 4bit system is so that there wouldn't be too much data loss but thank you for the suggesti…
Comment: Splice junctions plots for long-read seq data by alison.ludzki • 0
Thank you! I will check out miso!
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I did subsample the data to 30x coverage. I did run hifiasm on it, the log file did show some contents, but hifiasm ended again, stating th…
Comment: Tried building a compact sequence format with 4-bit storage by Alex Reynolds 36k
Using four bits for storage won't beat 2bit, of course, but direct access to a sequence of interest sounds interesting and useful and might…
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
Why don't you subsample your HiFi reads and try running hifiasm again? Maybe this will help if you have memory problems. However, I haven't…
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…
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