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121,903 results • Page 622 of 2439
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1.7k
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DEseq2: comparison the same when reversing factor order?
DESeq2 FCROS RNA-seq edgeR
4.2 years ago by gt ▴ 30
5
votes
2
replies
984
views
When NOT to trim adaptors?
exome trim adaptors
4.2 years ago by rtho ▴ 20
2
votes
4
replies
1.4k
views
Why are there nucleotides in the reference genome which are also minor alleles in the 1000 genomes project
reference genotype minor allele
updated 4.2 years ago by 48k • written 4.2 years ago by ▴ 420
1
vote
4
replies
1.9k
views
Finding the sex of an individual from an NGS output's alignment to a reference
coverage NGS samtools
4.2 years ago by langziv ▴ 70
3
votes
4
replies
2.0k
views
Using RefSeq gene annotation file to determine gene lengths
refseq rstudio htseq featurelength gtf fpkm geneid
updated 4.2 years ago by 9.3k • written 4.2 years ago by ▴ 20
0
votes
3
replies
1.7k
views
R extract gene names and protein descriptions from concatenated fasta headers
uniprot fasta R
updated 4.2 years ago by 21k • written 4.2 years ago by • 0
2
votes
1
reply
1.2k
views
Biopython SeqRecord alphabet compatibility
alphabet biopython
4.2 years ago by timothy.kirkwood ▴ 140
2
votes
1
reply
1.1k
views
How could I calculate r2 values between a list of SNPs with PLINK?
genomics plink snp r2
updated 4.2 years ago by 11k • written 4.2 years ago by ▴ 20
4
votes
4
replies
5.5k
views
Merge bgen,bgen.bgi,and .sample file from uk biobank
plink2 UKbiobank UKBB
4.2 years ago by okiedokie1208 ▴ 40
0
votes
0
replies
529
views
Software/Tool for aligning multiple nucleotide viral genome sequences (n=15; 300kb in length) while maintaining features/annotations?
multiple sequence alignment
4.2 years ago by Olivia • 0
1
vote
2
replies
2.2k
views
BioPython DSSP keyerror for a specific PDB file (1YYJ)
PDB Biopython DSSP
4.2 years ago by sajid ▴ 20
0
votes
2
replies
884
views
how to extract each two columns from a matrix with Talend?
talned
4.2 years ago by xinhui.wang ▴ 570
0
votes
0
replies
861
views
MAST with UMI data
scRNAseq Seurat MAST
4.2 years ago by Wocher33 ▴ 10
0
votes
3
replies
1.1k
views
highly correlated hidden factors
ATAC-Seq data exploration analysis
updated 3.4 years ago by • 0 • written 4.2 years ago by ▴ 120
0
votes
0
replies
764
views
Problem with CTCF motif orientation in Homer Motif DB
CTCF Motif Homer
4.2 years ago by data.lab.arr • 0
6
votes
5
replies
4.2k
views
Seurat scaling values not between 0 and 1
scRNA-seq scaling seurat
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 10
1
vote
0
replies
979
views
Job: Linux System Administrator for our Scientific Computing Platform at the IGTP, Barcelona
sysadmin linux hpc
updated 2.5 years ago by 45k • written 4.2 years ago by ★ 3.4k
0
votes
0
replies
666
views
News: Online training - Data Visualization with Python
Data visualization
4.2 years ago by Physalia-courses ★ 2.6k
1
vote
4
replies
3.0k
views
IGV batch scripts
IGV
4.2 years ago by bioinfo456 ▴ 150
0
votes
1
reply
614
views
Localization of Proteins / Localization of the translation process
localization genes
updated 4.2 years ago by 153k • written 4.2 years ago by • 0
0
votes
5
replies
2.4k
views
lmFit error - 'x' must be numeric
Limma expression R genes
4.2 years ago by Tushar • 0
5
votes
8
replies
4.4k
views
Snakemake. Problem with awk
awk Snakemake
4.2 years ago by kamanovae ▴ 100
1
vote
2
replies
1.0k
views
downloading manifest files on TCGA GDC
TCGA
4.2 years ago by peter ▴ 20
0
votes
0
replies
1.1k
views
Log transformation of relative abundance to visualize difference in small numbers for a heatmap
microbiome OTUs R log-transformation
4.2 years ago by almogangel • 0
1
vote
1
reply
864
views
Error in GMAP output SAM to covert BAM with PacBio reads
SAM to BAM GMAP PacBio
updated 4.2 years ago by 15k • written 4.2 years ago by • 0
0
votes
0
replies
542
views
Image as Tripal footer
tripal database footer
4.2 years ago by felipead66 ▴ 120
2
votes
2
replies
1.5k
views
Remove A List of Sequences from the MSA File
BAMtools SAMtools Multiple BWA BCFtools Alignment Sequence
4.2 years ago by Tastulek • 0
0
votes
4
replies
2.1k
views
GISTIC installation error
GISTIC2.0 CNV GISTIC
updated 4.2 years ago by 5.9k • written 4.2 years ago by ▴ 10
0
votes
2
replies
2.9k
views
How to get uniprot ID or protein length from Entrez gene id or gene name?
panther python David uniprot API
4.2 years ago by eranga114 • 0
0
votes
1
reply
1.6k
views
Job: Bioinformatics Training Specialist, HDC
Seattle
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 30
4
votes
4
replies
1.5k
views
How to perform alternative splicing from RNA Seq data?
RNA-Seq alternative-splicing
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 50
3
votes
2
replies
3.5k
views
What are the makeblastdb database files doing?
blastp database
4.2 years ago by timothy.kirkwood ▴ 140
1
vote
0
replies
728
views
Removing paralogs from multiple sequence alignments
sequencing BAM genomics comparative paralog
4.2 years ago by mglasena ▴ 40
0
votes
0
replies
665
views
Splitting predicted transcripts according to ORF coordinates
transcript ORF RNAseq
4.2 years ago by Buffo ★ 2.4k
3
votes
5
replies
1.7k
views
Collecting CDS from transcripts using Entrez
entrez biopython
updated 4.2 years ago by 153k • written 4.2 years ago by • 0
3
votes
6
replies
2.6k
views
how to align fastq files to a fasta file using biopython to produce VCF file
fastq biopython fasta VCF
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 20
2
votes
5
replies
1.5k
views
how to determine genes expressed in NK cells using DE RNA-Seq data
ImmGen NKcellgenes
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 40
3
votes
3
replies
3.4k
views
scRNAseq analysis with logNormCounts (scran/scuttle package) - log transformation with different log base?
scran log logNormCounts scuttle scRNAseq
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 150
0
votes
0
replies
1.3k
views
How not to overlap statistical symbols (asterisks) on a comparison with multiple groups boxplot (ggplot2) ?
asterisks ggplot2 boxplot stats multiplegroups
4.2 years ago by LuisNagano ▴ 90
0
votes
2
replies
900
views
Differential expression analysis
DEGs
updated 4.2 years ago by ▴ 390 • written 4.2 years ago by • 0
7
votes
9
replies
6.4k
views
Volcano plot from a RNAseq excel file
Volcanoplot
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
0
votes
0
replies
742
views
p.value of Fst calculate with snpgdsFst
snpgdsFst Fst
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
0
votes
4
replies
1.9k
views
how to align many single end fastq files from the same study on each other without using any reference genome using python?
fastq fasta python VCF
updated 4.2 years ago by 153k • written 4.2 years ago by ▴ 20
2
votes
1
reply
4.1k
views
Normalization after merging Seurat objects
Seq Seurat ScRNA-Seq RNA
updated 4.2 years ago by ★ 1.7k • written 4.2 years ago by ▴ 40
1
vote
6
replies
2.5k
views
convert Ensemble to HGNC symbols in a file with several columns
mariadb
4.2 years ago by storm1907 ▴ 30
0
votes
7
replies
1.9k
views
Ensembl Highlighted Exons Don't Match Coordinates
ensembl
updated 4.2 years ago by 24k • written 4.2 years ago by ▴ 840
3
votes
5
replies
1.6k
views
Biopython DSSP "unexpected sidechain number" Warning
PDB Biopython DSSP
4.2 years ago by sajid ▴ 20
0
votes
0
replies
1.0k
views
Treemix showing "ERROR: CH-JL does not have two alleles (expecting SNP data)"
Population SNP geneflow Treemix genetics
4.2 years ago by virtualinterlect • 0
0
votes
0
replies
574
views
Differential analysis on RNA-seq : Different results with two "equivalent" contrast matrix
design contrast rna-seq
updated 4.2 years ago by 22k • written 4.2 years ago by • 0
0
votes
1
reply
1.9k
views
Adding multiple RG values in Bowtie2 when aligning with multiple fastq
fastq group bowtie2 read
4.2 years ago by Runscar • 0
121,903 results • Page 622 of 2439
Recent Votes
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??
Comment: Is this PCA plot correct??
Subsetting before QC in Spatial Transcriptomics
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Recent Replies
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…
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Thomas.H.Hampton ▴ 10
Thanks again for your carefully considered reply. You asked what I am hoping to learn from a DE analysis. Autologous stem cells are well …
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi ATpoint, thank you very much for the helpful insight! I'm still doing some literature reading on this myself, but have you come across a…
Comment: Whole Genome Sequencing IG regions by ATpoint 89k
The question is what you are after. Is this a disease setup, or...well, what is this all about. Generally, these regions are hotspots of hy…
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