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822
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CPM or TPM values as discretization method input
RNA-Seq discretization TPM CPM
4.4 years ago by antmantras ▴ 80
3
votes
4
replies
2.9k
views
Expression of gene of interest across conditions in single-cell data
singlecell scater tpm seurat Rna-seq
4.4 years ago by kz • 0
0
votes
1
reply
1.5k
views
bbmap, mapq and uniquelly mapped reads filtering
alignment mapq
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 880
0
votes
3
replies
1.7k
views
Cell composition in each condition of single cell data
cell composition single-cell scProportionTest
4.4 years ago by paria ▴ 110
2
votes
6
replies
2.5k
views
Generate a file with SNPs given a WGS dataset
annotation snp ngs
4.4 years ago by iibrams07 ▴ 10
0
votes
0
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644
views
Calculate relative position of one range with respect to another
Bioconductor IRanges GenomicRanges R
4.4 years ago by Andrew • 0
0
votes
5
replies
2.3k
views
Limma experiment design and making contrasts
limma methylation 450k
4.4 years ago by kra277 • 0
6
votes
4
replies
4.0k
views
Keep values from VCF file into Ensembl VEP annotation
SNP
updated 3.6 years ago by ▴ 60 • written 4.7 years ago by ▴ 840
4
votes
6
replies
2.2k
views
Using outgroup in gene family dendograms
mega dendograms
4.4 years ago by Rogerio Ribeiro ▴ 110
0
votes
0
replies
2.0k
views
I can not get fasta file with the hit sequences running barrnap
barrnap bed
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 50
0
votes
1
reply
820
views
Raw read processing using trimmomatic
trimmomatic
updated 4.4 years ago by ▴ 880 • written 4.4 years ago by ▴ 10
2
votes
3
replies
1.8k
views
How to extract only the specific fasta sequences by matching the ID's to a different source files ?
RNA alignment DNA
updated 4.4 years ago by ★ 2.2k • written 4.4 years ago by ▴ 210
2
votes
2
replies
1.4k
views
Download discontinued gene record from NCBI via E-utils
E-utils NCBI Discondinued Gene
4.4 years ago by lmlukoseviciute ▴ 60
4
votes
6
replies
4.1k
views
Creating reference genome for mapping and then selecting
mm10 hg38 STAR RNA-seq
updated 4.4 years ago by 103k • written 4.4 years ago by ★ 2.8k
0
votes
2
replies
2.6k
views
ExomeDepth negative BF (bayesian factor) values meaning
WES DNA-seq CNV
updated 4.4 years ago by ★ 3.0k • written 4.6 years ago by ▴ 160
3
votes
2
replies
1.3k
views
Tool to find chromosome specific repeats
FISH repeats transposons genomics
updated 4.4 years ago by 56k • written 4.4 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Different results in limma if group is removed
limma edgeR
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 140
0
votes
2
replies
1.4k
views
LOOCV on limma results
loocv limma cross-validation
4.3 years ago by Palgrave ▴ 140
0
votes
0
replies
601
views
mtDNA variant calling
variant fasta seq mtdna
4.4 years ago by here_for_learning • 0
1
vote
4
replies
2.3k
views
How do I compare degree and betweenness centrality for different PPI networks?
PPI centrality degree Cytoscape network
4.4 years ago by gemmalouisebaldock ▴ 20
0
votes
5
replies
2.2k
views
What Coverage allele-fraction threshold to use?
allele-fraction snps
updated 23 months ago by 45k • written 4.4 years ago by ▴ 170
0
votes
2
replies
1.0k
views
Extracting transcripts from whole-transcriptome libraries
galaxy vcf rna-seq
4.4 years ago by julianneradford ▴ 20
1
vote
3
replies
2.0k
views
Prokka only creates .log file
miniconda prokka ubuntu bioconda
4.4 years ago by Camila Martínez ▴ 40
0
votes
0
replies
1.5k
views
News: Bioinformatics Open Source Conference 2021
OBF BOSC Conference
4.4 years ago by Chris Fields ★ 2.2k
4
votes
3
replies
3.7k
views
Hierarchical Clustering of GO terms
Clustering GO similarity Ontology
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 180
0
votes
1
reply
1.4k
views
TMM normalization for data across two sequencing batches
tmm normalization rnaseq
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 40
2
votes
2
replies
1.4k
views
Why we have exons that start and end at the same coordinate?!
gtf exon GRCh38
updated 4.4 years ago by 48k • written 4.4 years ago by 9.8k
2
votes
3
replies
1.1k
views
Microarray Error
R Microarray
4.5 years ago by rpazo001 ▴ 20
4
votes
7
replies
2.5k
views
Genotype Data in PLINK
Genotype PLINK
updated 4.4 years ago by ★ 4.8k • written 4.4 years ago by • 0
8
votes
2
replies
1.3k
views
How to extract fasta sequences and only its ID's, based on the subsequence fasta numbers from a main fasta file ?
fasta RNA DNA alignment
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 1000
0
votes
0
replies
691
views
Creating a comparison sequence for Multiple sequence alignment in Artemis Comparison Tool (ACT)
multiplesequencealignment artemis
updated 4.4 years ago by 35k • written 4.4 years ago by • 0
0
votes
0
replies
958
views
Calculate weighted and unwieghted Unifrac
R MEGA Unifrac
4.4 years ago by chiara.conte91 • 0
0
votes
0
replies
688
views
Error in discretizeDF.supervised(formula, data, method = disc.method) :data needs to be a data.frame
R arulesCBA
4.4 years ago by hebasamysaeid1 • 0
1
vote
3
replies
1.6k
views
Testing independence between 5' and 3' terminal sequences in a DNA database
sequence cluster DNA independence testing
updated 4.4 years ago by 103k • written 4.4 years ago by ▴ 640
1
vote
0
replies
1.4k
views
Job: Bioinformatics Research Analyst - Oncology
oncology genomics
4.2 years ago by Malachi Griffith 20k
7
votes
4
replies
4.6k
views
Visualizing & plotting variant reads within BAM files programmatically?
alignment
4.4 years ago by steve ★ 3.5k
0
votes
0
replies
558
views
Is there any method or algorithm to identify mutation using gene expression information?
algorithm mutation
4.4 years ago by Rida • 0
4
votes
6
replies
1.8k
views
How to extract sub fasta sequences from a multiline fasta file ?
RNA DNA
4.4 years ago by sunnykevin97 ▴ 1000
7
votes
5
replies
8.0k
views
How to convert multiple vcf files to a ped file?
plink vcftools
updated 4.4 years ago by 9.8k • written 9.1 years ago by ▴ 40
0
votes
0
replies
901
views
News: Online training: Data Visualization with Python
Python DataVisualization
4.4 years ago by Physalia-courses ★ 2.6k
2
votes
1
reply
843
views
Phylip/Paml alignment output file explanation ?
RNA alignment DNA
updated 4.4 years ago by ★ 2.2k • written 4.4 years ago by ▴ 1000
2
votes
8
replies
2.3k
views
BWA mapping quality 0 for all reads
mapping mapping_quality bwa
updated 4.4 years ago by 103k • written 4.4 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Pathway enrichment with z-scores
Transcriptomics GSEA NGS
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 320
0
votes
0
replies
773
views
Job: Biostatistician Job Opportunity (Bethesda, MD)
Genomics statistics Analysis Rstudio
4.4 years ago by christmasy • 0
1
vote
1
reply
4.9k
views
Removing duplicate varaints in PLINK
plink
updated 4.4 years ago by ▴ 30 • written 4.4 years ago by ▴ 10
1
vote
2
replies
1.2k
views
How to get Python code to run correctly for hetero-dimerization analysis
python sequence programming FASTA
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 320
11
votes
6
replies
2.1k
views
Forum: Is it still interesting to publish the profile of the transcriptome?
Article RNA Transcriptome Suggestion RNAseq
4.4 years ago by tiagobellintani ▴ 40
1
vote
3
replies
1.4k
views
How to extract de novo transcript from RNA long read alignement ?
RNA pacbio
updated 4.4 years ago by 9.3k • written 4.4 years ago by ★ 2.4k
4
votes
9
replies
8.6k
views
GATK Mutect2 Panel-Of-Normals generation
gatk mutect2 panel-of-normal wes non-tumor
updated 4.4 years ago by • 0 • written 5.2 years ago by ▴ 290
3
votes
4
replies
1.3k
views
How to split the header line into its components
Macspider
updated 4.4 years ago by 21k • written 4.4 years ago by • 0
121,904 results • Page 675 of 2439
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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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