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519 results • Page 2 of 11
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1
vote
5
replies
338
views
samtools filtering
samtools
updated 15 days ago by ★ 1.2k • written 22 days ago by ▴ 80
1
vote
5
replies
265
views
Downsampling fastq file
downsample fastq
updated 3 days ago by 43k • written 3 days ago by ▴ 80
0
votes
5
replies
333
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate BUSCO.
updated 21 days ago by 141k • written 21 days ago by ▴ 10
0
votes
5
replies
488
views
How to assure that sequence consensus is genuine?
genome
19 days ago by marongiu.luigi ▴ 710
3
votes
5
replies
408
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
updated 23 days ago by 141k • written 23 days ago by ▴ 200
2
votes
5
replies
1.6k
views
Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata functional-annotation BRAKER MAKER
updated 24 days ago by ▴ 40 • written 15 months ago by ▴ 60
0
votes
5
replies
420
views
Error running local blastn in R using system2
blastn NCBI R
28 days ago by Harrison • 0
2
votes
5
replies
450
views
Marking duplicates using UMIs
Deduplication UMI
updated 4 days ago by 19k • written 5 days ago by • 0
0
votes
5
replies
290
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
2 days ago by njornet ▴ 20
2
votes
5
replies
444
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
9 days ago by Bikram Kumar • 0
2
votes
5
replies
685
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 5 days ago by ▴ 740 • written 6 days ago by ★ 2.4k
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 6 days ago by • 0 • written 6.5 years ago by ▴ 30
0
votes
5
replies
1.2k
views
RNAseq differential gene expression analysis yield results which come from digestive content
differential-gene-expression RNA-Seq
updated 16 days ago by 43k • written 6.4 years ago by ▴ 90
0
votes
5
replies
401
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 16 days ago by 141k • written 16 days ago by • 0
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 15 days ago by • 0 • written 3.8 years ago by ★ 1.8k
0
votes
5
replies
1.6k
views
what does mean this error ? "(ERR): hisat2-align exited with value 1" in mapping long noncoding RNAs
long-non-coding-RNA lncRNA
updated 20 days ago by 43k • written 2.6 years ago by • 0
0
votes
5
replies
291
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 1 day ago by 141k • written 2 days ago by ▴ 90
0
votes
5
replies
1.8k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing illumina
updated 17 days ago by 3.2k • written 3.4 years ago by • 0
1
vote
4
replies
344
views
How to get human-mouse conservation score from UCSC
conservation mouse IGV human score
21 days ago by diqixiaoyaoer ▴ 10
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 7 days ago by 43k • written 7.1 years ago by ▴ 310
0
votes
4
replies
337
views
Compute bootstrap values on consensus tree
phylogeny tree raxml
11 days ago by pablo ▴ 300
0
votes
4
replies
1.1k
views
Getting biological replicates from SRA run NCBI
fastq AWS SRA RNAseq
24 days ago by Andres ▴ 20
2
votes
4
replies
395
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 16 days ago by 141k • written 17 days ago by • 0
0
votes
4
replies
316
views
Questions about transfering wgs file to reference genome file
fasta cram genome
14 days ago by me • 0
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 8 days ago by 43k • written 4.8 years ago by ▴ 10
0
votes
4
replies
318
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq STAR IGV
29 days ago by rohitsatyam102 ▴ 850
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 8 days ago by 43k • written 4.7 years ago by ▴ 10
2
votes
4
replies
293
views
Addmetadata to seurat obj
seurat
15 days ago by synat.keam ▴ 100
1
vote
4
replies
1.3k
views
Splitting long reads into shorter chunks
long-read
updated 20 days ago by 43k • written 5.8 years ago by ▴ 60
1
vote
4
replies
812
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing wgs
16 days ago by Hyper_Odin ▴ 310
0
votes
4
replies
1.8k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq batch-effect R
updated 8 days ago by 43k • written 4.8 years ago by ▴ 20
1
vote
4
replies
280
views
Removing batch effect using combat-seq
batch effect RNA-Seq combat-seq
updated 24 days ago by ★ 1.7k • written 25 days ago by • 0
0
votes
4
replies
577
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
7 days ago by Kai Xin • 0
1
vote
4
replies
389
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics htseq-count RNA-Seq NGS hisat2
updated 13 days ago by ★ 1.7k • written 14 days ago by • 0
0
votes
4
replies
402
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
28 days ago by BRENO • 0
4
votes
4
replies
359
views
Average expression of a sample in single-cell data
single-cell rna-seq
24 days ago by newuser2024 • 0
2
votes
4
replies
303
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP CPU transcriptomics
28 days ago by Mohamed Abderrahmane ▴ 20
0
votes
4
replies
275
views
Adaptive sampling for whole chromosomes
T2T Nanopore AdaptiveSampling aneuploidy centromeres
16 days ago by njornet ▴ 20
2
votes
4
replies
262
views
interpretartion of a vcf file
calling genotype ONT variant diploid
2 days ago by samuelkalandarov2002 ▴ 10
0
votes
4
replies
250
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
1 day ago by sehriban.buyukkilic ▴ 10
0
votes
4
replies
332
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 15 days ago by 141k • written 17 days ago by • 0
1
vote
4
replies
365
views
Molecular docking with Autodock
Docking proteomics
updated 20 days ago by 43k • written 12 weeks ago by ▴ 10
2
votes
4
replies
316
views
SnpEff annotates coding duplication as intronic?
snpeff
9 days ago by kirill.zaslavsky • 0
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 7 days ago by 43k • written 18 months ago by • 0
3
votes
4
replies
353
views
Single cell analysis with "meta".tsv.gz file
Single-cell
23 days ago by Estevão • 0
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq RNA-Seq batch-effect DESeq2
updated 8 days ago by 43k • written 5.1 years ago by ★ 2.6k
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression RNA-Seq DESeq2
updated 16 days ago by 43k • written 8.1 years ago by ▴ 80
0
votes
4
replies
502
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx deconcolution
8 days ago by feather-W • 0
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID org.Dr.eg.db
updated 9 days ago by 43k • written 5.5 years ago by ▴ 170
0
votes
3
replies
217
views
Peptide identification from Mass spec data
Transcriptomics Proteins Mass-spec
updated 21 days ago by 43k • written 22 days ago by ▴ 10
519 results • Page 2 of 11
Recent Votes
Comment: genome assembly records not present in assembly_summary.txt
Comment: genome assembly records not present in assembly_summary.txt
Answer: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
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Recent Replies
Comment: genome assembly records not present in assembly_summary.txt by sapuizait ▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question by bk11 ★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon by GenoMax 141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely mapping in regions whe…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File? by cmdcolin ★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon by Patadu94 • 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon by Patadu94 • 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq by pinheirofabiano ▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon by Patadu94 • 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Pierre Lindenbaum 161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J • 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question by starswillfade ▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question by starswillfade ▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Comment: genome assembly records not present in assembly_summary.txt by GenoMax 141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto) by i.sudbery 19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File? by benformatics 3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
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