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531 results • Page 1 of 11
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7
votes
8
replies
1.6k
views
How can we time a recent gene duplication event using (neutral?) DNA mutations as molecular clock?
molecular-clock gene-duplication phylogeny
updated 1 day ago by 37k • written 7.7 years ago by ▴ 20
7
votes
4
replies
1.3k
views
microarray gene datasets
gene
updated 1 day ago by 37k • written 7.7 years ago by ▴ 60
6
votes
9
replies
336
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
error BAM Bowtie
updated 3 days ago by 125k • written 8 days ago by ▴ 40
5
votes
7
replies
3.0k
views
STAR aligner pauses frequently during mapping
rna-seq STAR
updated 3 days ago by 37k • written 7.7 years ago by • 0
5
votes
2
replies
2.2k
views
Cut & run - bowtie2 dovetail option
cut and run dovetail bowtie2
updated 4 days ago by • 0 • written 2.3 years ago by ▴ 270
5
votes
2
replies
315
views
30 bp sequence that does not show hit within a genome
similarity
updated 29 days ago by 7.8k • written 29 days ago by ▴ 370
5
votes
14
replies
650
views
How to Calulate Allele Frequency from a VCF File?
frequency allele VCF
updated 3 days ago by 21k • written 7 days ago by • 0
4
votes
6
replies
761
views
Differentially gene expression multispecies
Expression Multispecies Rnaseq differentially
updated 14 days ago by ▴ 10 • written 18 months ago by ▴ 40
4
votes
4
replies
744
views
Analysis of Nanopore cDNA sequencing data
alignment nanopore sequencing minimap2
7 days ago by Nico80 ▴ 60
4
votes
2
replies
2.1k
views
dbFetch from EBI with bogus accession number returns valid record
EBI dbFetch
updated 28 days ago by 37k • written 7.7 years ago by 2.3k
4
votes
2
replies
2.3k
views
Signal Distribution Charts
ChIP-Seq next-gen R
updated 3 days ago by 37k • written 7.7 years ago by 13k
4
votes
8
replies
707
views
Proteomic Statistics - FDR vs p-value
FDR proteomics t-test p-value
17 days ago by bhumm ▴ 20
4
votes
11
replies
2.5k
views
Please add an explicit type tag :NAME
software-error next-gen genome
updated 3 days ago by 37k • written 4.7 years ago by ▴ 30
4
votes
1
reply
185
views
RNA seq analysis from the data file which received from company
RNA editing
updated 10 days ago by 2.6k • written 10 days ago by • 0
4
votes
10
replies
3.5k
views
TCGA normalized count data of 1000 samples for DGE
RNA-Seq TCGA
updated 10 days ago by 37k • written 7.8 years ago by ▴ 460
4
votes
2
replies
185
views
Analyzing bulk RNA-seq
RNAseq
updated 1 day ago by 13k • written 1 day ago by • 0
4
votes
8
replies
1.9k
views
Select only sequences that align with X% of a query during blastp search
sequence blast alignment
updated 10 days ago by 37k • written 7.7 years ago by ★ 2.7k
3
votes
4
replies
1.5k
views
getting reference genome accession number
RNA-Seq
updated 2 days ago by 37k • written 7.7 years ago by ★ 4.1k
3
votes
7
replies
1.9k
views
problem with genome viewer IGV
IGV mapping BAM
updated 29 days ago by 125k • written 4.6 years ago by • 0
3
votes
4
replies
398
views
Changing Temporary File Location for Local BLASTP to nr Database
temporary blast file protein nr
16 days ago by katieostrouchov ▴ 20
3
votes
0
replies
2.1k
views
Informations about UCSC bigWigCorrelate tools
bigwig ucsc
updated 2 days ago by 37k • written 7.7 years ago by ▴ 30
3
votes
4
replies
321
views
Renaming fasta headers based on a list
fasta
updated 21 days ago by 37k • written 22 days ago by • 0
3
votes
6
replies
570
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
12 days ago by TN • 0
3
votes
1
reply
189
views
LMM GWAS - why are population covariates included?
LMM GWAS population-covariates
updated 29 days ago by 37k • written 29 days ago by ▴ 20
3
votes
5
replies
6.2k
views
Converting Vcftools output to R readable format
vcf SNP R vcftools
updated 11 days ago by 37k • written 7.7 years ago by ▴ 100
3
votes
4
replies
480
views
R package DESeq2 in R 3.5.1
packages installing error R
25 days ago by sehriban.buyukkilic • 0
3
votes
3
replies
428
views
GO analysis: Different results EnrichGO vs ShinyGO
enrichGO GO RNA-seq shinyGO analysis
updated 23 days ago by 26k • written 25 days ago by ▴ 10
3
votes
3
replies
2.6k
views
Breast cancer TCGA data - DGE analysis
RNA-Seq Voom Raw_Count TCGA
updated 14 days ago by 37k • written 7.7 years ago by ▴ 460
3
votes
2
replies
2.4k
views
Creating neo4j graph databases from UCSC tables browser
neo4j graph-database
updated 15 days ago by 37k • written 7.7 years ago by 13k
3
votes
6
replies
2.0k
views
snpEff suitable for Bathycoccus prasinos?
protist non-human SNP annotation
updated 4 days ago by 37k • written 7.8 years ago by ▴ 10
3
votes
2
replies
164
views
WGCNA gene selection: gene significance or LASSO?
LASSO WGCNA
updated 1 day ago by 11k • written 2 days ago by • 0
3
votes
2
replies
1.5k
views
parsing the samtools view out put
RNA-Seq
updated 8 hours ago by 37k • written 7.7 years ago by ★ 4.1k
3
votes
6
replies
203
views
Which file and data structure is used to create volcano plot from scRNA-Seq experiment?
plot Volcano
8 hours ago by Chris ▴ 60
3
votes
4
replies
477
views
Snakemake not executing any tasks
python readqc Snakemake cutadapt
updated 27 days ago by ▴ 450 • written 29 days ago by ▴ 20
2
votes
4
replies
214
views
Calculate sequencing file size?
storage data sequencing plan management
updated 8 days ago by 125k • written 8 days ago by ★ 1.2k
2
votes
4
replies
272
views
Retrieve specific fasta sequences from a group of assemblies
CDS gene sequence
4 days ago by SushiRoll ▴ 100
2
votes
1
reply
1.2k
views
pair wise differences of different populations
snp
updated 10 days ago by 37k • written 7.7 years ago by • 0
2
votes
3
replies
746
views
Merging FASTQs from the same sample
Merging FASTQ cellranger scRNAseq 10X
updated 5 days ago by • 0 • written 13 months ago by • 0
2
votes
7
replies
640
views
When I run Trimmomatic, I continue to get an "unknown trimmer" error and cannot figure out how to fix it.
trimmomatic
updated 21 days ago by 37k • written 23 days ago by • 0
2
votes
1
reply
377
views
In GWAS what is the point of regressing a quantitative phenotype on covariates first and taking the residuals?
gwas
updated 22 days ago by 1.8k • written 22 days ago by ▴ 720
2
votes
3
replies
293
views
What should be control group for differential expression in single cell? either distant normal samples or primary tumors when analysing metastatic sa…
single-cell transcriptomics differential-expression RNAseq
updated 10 days ago by 68k • written 10 days ago by ▴ 30
2
votes
4
replies
363
views
Change sample ID in BAM file to cell barcode
bam samtools barcode scrna
11 days ago by martin.grasshoff • 0
2
votes
3
replies
10k
views
converting maf to vcf
Exome maf2vcf
updated 11 days ago by 37k • written 7.7 years ago by • 0
2
votes
4
replies
341
views
Differences between genomic position and genomic loci?
loci dna genome genetics gene
25 days ago by DS ▴ 20
2
votes
7
replies
6.6k
views
Bowtie2 run out of memory
software-error alignment bowtie2
updated 13 hours ago by 37k • written 7.7 years ago by ▴ 50
2
votes
6
replies
435
views
Predicting protein fold using known stracture
protein modeller prediction 3D
updated 23 days ago by 52k • written 23 days ago by ▴ 270
2
votes
12
replies
4.1k
views
Adding barcodes to forward and reverse reads after sequencing
obitools barcoding next-gen-sequencing
updated 13 hours ago by 37k • written 7.7 years ago by ▴ 20
2
votes
2
replies
3.0k
views
Does RPKM value of TCGA data need to be normalized by reference gene?
RNA-Seq
updated 29 days ago by 37k • written 7.7 years ago by ▴ 10
2
votes
2
replies
411
views
Gene coverage plots from a data frame on tiling amplicon sequencing data
visualization coverage sequencing plots R
26 days ago by pramach1 ▴ 30
2
votes
0
replies
196
views
Should one concatenate two haplotype genome assemblies into one assembly?
PacBio genome-assembly whole-genome-sequence Hi-C
updated 1 day ago by 37k • written 11 months ago by ▴ 150
531 results • Page 1 of 11
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Answer: Remove mitochondrial reads from BAM files
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Comment: Analyzing bulk RNA-seq
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Recent Replies
Comment: Diffbind losing peaks when going from small to larger consensus peak set by tara.mcintyre • 0
I'm now realizing it might be due to the filter parameter being set =1 when I run dba.count because when I set it to 0, all of the peaks ar…
Answer: Obtaining every"Protein ID" from a genome in OMA by clement.train ▴ 40
Hello, It seems that the current download is limited to 100 genes on the genomes pages, we will increase this limit to the extent of ea…
Comment: DNA methylation (RRBS/WGBS) prediction from DNA sequence (WGS) by Lalaland ▴ 10
Thank you very much, Matthias! I will definitely check those links out myself!
Comment: RNA Editing data from RNA-seq by Juke34 7.5k
What tool did you look at ?
Comment: want the codes for Deseq2 to perform DEGs. by rupali • 0
thanks for help
Comment: cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11 by Yingying • 0
Hi, Yes I've uploaded the diagnostic file to 10x support already, but haven't got any response yet.
Comment: cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11 by GenoMax 125k
You may want to contact 10x tech support. When this process failed it must have created a diagnostic archive. You also get a message about …
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files? by jv ▴ 780
`bedtools intersect -v` is one option for identifying the unique genes from the older gene model. <https://bedtools.readthedocs.io/en/lates…
Comment: Alien-hunter outputs by schlogl ▴ 130
@GenoMax Hope this helps...Thank you
Comment: DESeq2 results function runs very slow on Windows 10 by ATpoint 68k
Does it go away if you remove the `parallel` from `results()`? After all, it is the `DESeq()` function that is the bottleneck when n is lar…
Comment: HTSeq error processing GFF file by ibq.enriquepola • 0
enrique@L:~/bioinformatica/index/prueba$ head -n 997531 GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.gff|tail -n 1 NC_007982.1 Ref…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe by Chris ▴ 60
Thank you for your help! I got an error that I could not find the solution on the Internet: library(EnhancedVolcano) Loading required…
Comment: HTSeq error processing GFF file by barslmn ★ 1.2k
I guess you can try to replace the "?" to a "." Also, you can copy and paste text instead of the screenshots?
Answer: DESeq2 results function runs very slow on Windows 10 by Istvan Albert 96k
Note the following: https://support.bioconductor.org/p/115415/ it looks like it has to do with the Parallel=TRUE flag
Comment: DESeq2 results function runs very slow on Windows 10 by GenoMax 125k
> there is a massive difference in performance between them. It still is taking only one minute.
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