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546 results • Page 2 of 11
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2
votes
5
replies
1.6k
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Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata functional-annotation BRAKER MAKER
updated 22 days ago by ▴ 40 • written 15 months ago by ▴ 60
2
votes
5
replies
418
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
6 days ago by Bikram Kumar • 0
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 3 days ago by • 0 • written 6.5 years ago by ▴ 30
1
vote
5
replies
180
views
Downsampling fastq file
downsample fastq
updated 1 day ago by 43k • written 1 day ago by ▴ 80
0
votes
5
replies
409
views
Error running local blastn in R using system2
blastn NCBI R
25 days ago by Harrison • 0
1
vote
5
replies
404
views
Marking duplicates using UMIs
Deduplication UMI
updated 1 day ago by 19k • written 2 days ago by • 0
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 14 days ago by 43k • written 6.4 years ago by ▴ 90
0
votes
5
replies
328
views
Incongruencies in GT assignment by Freebayes
depth freebayes heterozygous genotype
18 days ago by virginia.baraja • 0
0
votes
5
replies
482
views
How to assure that sequence consensus is genuine?
genome
17 days ago by marongiu.luigi ▴ 710
0
votes
5
replies
2.0k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq batch-effect normalization
updated 6 days ago by 43k • written 20 months ago by ▴ 60
0
votes
5
replies
320
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate BUSCO.
updated 19 days ago by 141k • written 19 days ago by ▴ 10
0
votes
5
replies
393
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 13 days ago by 141k • written 14 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 12 days ago by • 0 • written 3.8 years ago by ★ 1.8k
2
votes
5
replies
662
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 3 days ago by ▴ 740 • written 4 days ago by ★ 2.4k
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 18 days ago by 43k • written 2.6 years ago by • 0
0
votes
5
replies
284
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 19 days ago by 43k • written 22 days ago by ▴ 150
0
votes
5
replies
374
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
19 days ago by Srinka ▴ 20
3
votes
5
replies
404
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
updated 20 days ago by 141k • written 21 days ago by ▴ 200
0
votes
4
replies
1.1k
views
Getting biological replicates from SRA run NCBI
fastq AWS SRA RNAseq
22 days ago by Andres ▴ 20
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq RNA-Seq batch-effect DESeq2
updated 6 days ago by 43k • written 5.1 years ago by ★ 2.6k
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 6 days ago by 43k • written 4.8 years ago by ▴ 10
3
votes
4
replies
345
views
Single cell analysis with "meta".tsv.gz file
Single-cell
20 days ago by Estevão • 0
1
vote
4
replies
274
views
Removing batch effect using combat-seq
batch effect RNA-Seq combat-seq
updated 22 days ago by ★ 1.7k • written 22 days ago by • 0
1
vote
4
replies
1.3k
views
Splitting long reads into shorter chunks
long-read
updated 18 days ago by 43k • written 5.8 years ago by ▴ 60
2
votes
4
replies
287
views
Addmetadata to seurat obj
seurat
13 days ago by synat.keam ▴ 100
0
votes
4
replies
1.8k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq batch-effect R
updated 6 days ago by 43k • written 4.8 years ago by ▴ 20
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 6 days ago by 43k • written 4.7 years ago by ▴ 10
4
votes
4
replies
354
views
Average expression of a sample in single-cell data
single-cell rna-seq
21 days ago by newuser2024 • 0
2
votes
4
replies
299
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP CPU transcriptomics
25 days ago by Mohamed Abderrahmane ▴ 20
1
vote
4
replies
381
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics htseq-count RNA-Seq NGS hisat2
updated 10 days ago by ★ 1.7k • written 11 days ago by • 0
0
votes
4
replies
311
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq STAR IGV
26 days ago by rohitsatyam102 ▴ 840
0
votes
4
replies
486
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx deconcolution
5 days ago by feather-W • 0
0
votes
4
replies
267
views
Adaptive sampling for whole chromosomes
T2T Nanopore AdaptiveSampling aneuploidy centromeres
13 days ago by njornet ▴ 20
0
votes
4
replies
2.7k
views
MACS2 BAMPE and BEDPE gave dramatically different "mean fragment size"
ChIP-Seq
updated 29 days ago by • 0 • written 6.5 years ago by • 0
2
votes
4
replies
304
views
SnpEff annotates coding duplication as intronic?
snpeff
6 days ago by kirill.zaslavsky • 0
0
votes
4
replies
301
views
Questions about transfering wgs file to reference genome file
fasta cram genome
12 days ago by me • 0
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression RNA-Seq DESeq2
updated 14 days ago by 43k • written 8.0 years ago by ▴ 80
0
votes
4
replies
567
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
4 days ago by Kai Xin • 0
0
votes
4
replies
324
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 12 days ago by 141k • written 14 days ago by • 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 5 days ago by 43k • written 18 months ago by • 0
0
votes
4
replies
395
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
25 days ago by BRENO • 0
2
votes
4
replies
390
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 13 days ago by 141k • written 14 days ago by • 0
1
vote
4
replies
340
views
How to get human-mouse conservation score from UCSC
conservation mouse IGV human score
18 days ago by diqixiaoyaoer ▴ 10
1
vote
4
replies
801
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing wgs
13 days ago by Hyper_Odin ▴ 310
0
votes
4
replies
333
views
Compute bootstrap values on consensus tree
phylogeny tree raxml
8 days ago by pablo ▴ 300
0
votes
4
replies
163
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
updated 5 hours ago by 141k • written 8 hours ago by ▴ 20
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 5 days ago by 43k • written 7.1 years ago by ▴ 310
1
vote
4
replies
357
views
Molecular docking with Autodock
Docking proteomics
updated 18 days ago by 43k • written 11 weeks ago by ▴ 10
0
votes
3
replies
334
views
Resources regarding Proteomics (In-Silico)
molecular-simulation docking protein proteomics
updated 21 days ago by 43k • written 5 weeks ago by • 0
1
vote
3
replies
145
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
10 hours ago by WouterDeCoster 47k
546 results • Page 2 of 11
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C: Threshold over percentage identity in blastn
A: Threshold over percentage identity in blastn
The Biostar Herald for Tuesday, April 23, 2024
Answer: Including plasmid in transcriptome assemblies
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
RNA-seq power estimation using ssizeRNA program
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Comment: TCGA2STAT Error: Firehose connection by Ngrin • 0
Yeah makes sense. I was following their github. Thanks for pointing this out.
Comment: The Biostar Herald for Tuesday, April 23, 2024 by Pierre Lindenbaum 161k
bwa 0.7.18 released ! https://github.com/lh3/bwa/releases/tag/v0.7.18
Comment: Downsampling fastq file by Ram 43k
I'm moving this to a comment for now.
Answer: Seurat merge and batch correction by bk11 ★ 2.3k
You can merge your seven Seurat objects and perform integration using **Seurat V5** to remove the batch effect- ```r library(Seurat) libra…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
Yeah, I've been digging around the web for a while now. Can't find any information about the barcodes. The total number of combinations is …
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
Ah I see that in now. I am not sure why MGI has split the whitelist into two sections. You may need to see if you can dig up some info abou…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
read 1 is 30bp... which I think you meant to type. If you scroll approximately halfway down the json file I linked to, it has the following…
Comment: TCGA2STAT Error: Firehose connection by Ram 43k
The package has been removed from CRAN and BioConductor. Should you even be using it?
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
The barcodes are in location 1-10 and you have the actual list there. I don't know for certain what is in position 11-20 (perhaps spacer, c…
Answer: Including plasmid in transcriptome assemblies by GenoMax 141k
> I want to use both STAR and BOWTIE2 for assembly Those programs are aligners not assemblers. But since you are working with bacteria yo…
Comment: How to slice a gvcf file with tabix? by Sd • 0
I already have gvcfs called by chromosome and there are 24 gvcfs per sample which I merged them into a single gvcf per sample. Now I want …
Comment: Find subcluster under a cluster, find differential genes in one cluster between by bk11 ★ 2.3k
First, could you please explain any reason for not using Seurat V5 approach for your data integration mentioned in [here][1]? > Now moving…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
So I'd take the json file located [here][1] and essentially create the whitelist to be all possible combinations of the position 1-10 barco…
Comment: TCGA2STAT Error: Firehose connection by Ngrin • 0
Hey Gnana, could you find a way to solve the issue? I have the same error
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
You simply need to make a list of barcodes one on each line: https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-wh…
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