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6,936 results • Page 6 of 139
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15
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12
replies
1.4k
views
6 follow
Forum: New Macbook M4 laptops (Pro vs Max)
Pro Max Mac RNA-Seq M4
updated 20 days ago by ★ 7.2k • written 22 days ago by ▴ 10
5
votes
12
replies
8.5k
views
how to run freebayes in multi-thread
VCF freebayes multi-thread
updated 3 months ago by 148k • written 5.9 years ago by ▴ 730
9
votes
12
replies
4.9k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 9 months ago by 44k • written 5.7 years ago by ▴ 330
54
votes
12
replies
29k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 9 months ago by • 0 • written 12.8 years ago by ★ 2.9k
0
votes
12
replies
1.3k
views
BWA MEM different synthax on linux (bash) and macOS (zsh)
MEM BWA
10 months ago by gernophil ▴ 120
7
votes
12
replies
1.4k
views
ensembl - selecting SNPs of specific genes
SNP VCF ensembl gene genome
11 months ago by Eliza ▴ 30
1
vote
12
replies
6.0k
views
7 follow
Error in CIBERSORTx
RNA-seq CIBERSORT LM22
updated 11 weeks ago by • 0 • written 2.3 years ago by • 0
0
votes
12
replies
1.0k
views
Creating a sample specific directory on the go while using -wget command to download the files
wget ncbi
updated 6 months ago by 44k • written 6 months ago by • 0
10
votes
12
replies
2.7k
views
Tool: PanDepth, an ultra-fast and efficient genomic tool for coverage calculation
bam paf depth cram coverage
11 months ago by Huiyang ▴ 200
3
votes
12
replies
5.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 8 months ago by ▴ 180 • written 3.7 years ago by ▴ 20
6
votes
12
replies
4.0k
views
RNAseq reads contamination
RNA-Seq
updated 7 months ago by ▴ 10 • written 7.2 years ago by ▴ 610
11
votes
12
replies
15k
views
11 follow
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
updated 10 months ago by ★ 2.1k • written 4.8 years ago by ▴ 60
1
vote
12
replies
1.5k
views
6 follow
blast Segmentation fault
blastn fasta local-blast
updated 7 months ago by 44k • written 10 months ago by ▴ 20
8
votes
12
replies
2.2k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
9 months ago by Ram 44k
2
votes
12
replies
3.7k
views
WCGNA installation help
R WGCNA
updated 11 months ago by 44k • written 5.7 years ago by • 0
3
votes
12
replies
1.9k
views
Problem running scPred
scPred scPredict
updated 6 weeks ago by 44k • written 12 months ago by • 0
5
votes
12
replies
6.5k
views
how can i download human ribosomal reference ?
RNA-Seq rRNA
updated 5 weeks ago by ▴ 430 • written 5.7 years ago by ▴ 70
4
votes
12
replies
748
views
Transcript coverage 3' bias. Is it really that determining?
mappings transcriptome RNA
updated 5 weeks ago by 21k • written 5 weeks ago by ▴ 10
5
votes
12
replies
2.9k
views
Predicted RefSeq genes
gene genome
updated 6 months ago by 44k • written 8.4 years ago by • 0
3
votes
12
replies
1.1k
views
struggle to get fasta files from ucsc goldenPath
ucsc getfasta fasta
9 months ago by Lila M ★ 1.3k
8
votes
12
replies
4.4k
views
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
ATAC-seq
updated 9 months ago by • 0 • written 4.1 years ago by ▴ 40
14
votes
12
replies
48k
views
7 follow
Help interpreting BLAST results? (Max score/Percent. Identity/E-values)
alignment gene genome
updated 22 days ago by ▴ 150 • written 4.3 years ago by ▴ 20
7
votes
12
replies
1.2k
views
Custom Genome Curation in IGV
IGV
updated 6 months ago by ★ 1.3k • written 6 months ago by ▴ 20
3
votes
12
replies
1.5k
views
bbmap read length from fastq
fastq bbmap
updated 10 months ago by 148k • written 10 months ago by ▴ 160
0
votes
12
replies
2.5k
views
6 follow
GATK3 error message
GATK next-gen
updated 3 months ago by 44k • written 6.6 years ago by ▴ 60
9
votes
12
replies
1.6k
views
Is it possible to access the code of a bioinformatics article?
publication
updated 12 months ago by ★ 1.2k • written 12 months ago by ▴ 50
7
votes
12
replies
1.6k
views
ORA with clusterProfiler
clusterProfiler ORA
updated 7 days ago by ▴ 130 • written 13 months ago by ▴ 170
38
votes
12
replies
19k
views
8 follow
BEDOPS gtf2bed conversion error with Ensembl GTF
gtf2bed ensembl bedops gtf
updated 10 months ago by 36k • written 8.4 years ago by ▴ 260
2
votes
12
replies
1.8k
views
Nanopore data filtering using fastp
fastp nanopore
9 months ago by emilydolivo97 ▴ 10
6
votes
11
replies
3.8k
views
6 follow
User friendly (visual&interactive) VCF/BCF mining tools (2021)
gui vcf
updated 6 months ago by ▴ 10 • written 3.3 years ago by ★ 5.3k
4
votes
11
replies
855
views
Counts after using feature counts is low
hisat2 featureCounts lowcounts
updated 6 weeks ago by 148k • written 6 weeks ago by ▴ 20
4
votes
11
replies
2.2k
views
Paired layout, but one fastq file
fastq
updated 9 months ago by 148k • written 22 months ago by ▴ 120
3
votes
11
replies
4.9k
views
7 follow
How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by cell barcode?
10xgenomics RNAseq scRNA CB
updated 5 months ago by 148k • written 2.5 years ago by ▴ 20
4
votes
11
replies
2.1k
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r ComplexHeatmap
updated 7 months ago by 44k • written 8 months ago by • 0
4
votes
11
replies
1.4k
views
RNA-seq differentially expressed genes (DEGs) with low fold change values
ComBat-seq RNA-seq DESeq2 DEGs
updated 7 months ago by 14k • written 7 months ago by • 0
4
votes
11
replies
1.3k
views
Remove X in row name with only number
GSVA
updated 11 months ago by 44k • written 11 months ago by ▴ 340
2
votes
11
replies
1.4k
views
KeepBothReads in Trimmomatic
Trimmomatic PE-reads
3 months ago by mariannapauletto ▴ 90
4
votes
11
replies
1.6k
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
8 months ago by J ▴ 10
3
votes
11
replies
1.4k
views
6 follow
How to solve DESeq2 Error in checkFullRank(modelMatrix) cause by biological replicates information?
DESEq2 DESEq
updated 5 months ago by 14k • written 5 months ago by • 0
25
votes
11
replies
4.2k
views
6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 9 months ago by 44k • written 15.3 years ago by 102k
0
votes
11
replies
1.2k
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
8 months ago by Tuck898 • 0
7
votes
11
replies
990
views
Sankey + dot plot
R sankey gene-ontology GO
updated 3 months ago by ★ 2.6k • written 3 months ago by • 0
5
votes
11
replies
878
views
6 follow
Asking for parallel jobs setting on HPC when analyzing sequencing data
HPC parallel
updated 7 months ago by 4.7k • written 7 months ago by ▴ 70
1
vote
11
replies
782
views
Use R to Produce CpG Information
R CpG
5 months ago by Dana • 0
2
votes
11
replies
3.2k
views
How to extract unmapped mate for specific reads using pysam or other module in python?
pysam
updated 6 months ago by 21k • written 2.2 years ago by ▴ 10
16
votes
11
replies
2.0k
views
7 follow
How I know if it is a batch effect or are real differences between my controls and treatments?
RNA-seq Transcriptomics ComBat-seq Batch-Effect
updated 9 months ago by 148k • written 9 months ago by ▴ 20
2
votes
11
replies
9.1k
views
Merging multiple samples in Seurat
scRNA-seq snRNA-seq RNA-seq Seurat
updated 5 months ago by ▴ 10 • written 15 months ago by • 0
5
votes
11
replies
854
views
Determine type of Pacbio read
sratoolkit CLR Pacbio Hifi long-reads
updated 4 weeks ago by 148k • written 4 weeks ago by ▴ 10
19
votes
11
replies
3.4k
views
Unable to Create Index file of VCF
VCF
updated 4 months ago by 148k • written 23 months ago by ▴ 140
5
votes
11
replies
1.2k
views
6 follow
Conversion of Gene Name to Ensembl ID
Ensembl RNA-Seq
updated 6 months ago by 4.5k • written 6 months ago by • 0
6,936 results • Page 6 of 139
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Comment: STAR aligner - Is this still maintained?
Answer: drug sensitivity prediction
A: How Do I Convert Fbgn (Flybase Ids) To Gene Symbols In R/Bioconductor?
How Do I Convert Fbgn (Flybase Ids) To Gene Symbols In R/Bioconductor?
Answer: STAR aligner - Is this still maintained?
Answer: STAR aligner - Is this still maintained?
Answer: STAR aligner - Is this still maintained?
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Comment: STAR aligner - Is this still maintained? by ATpoint 86k
Definitely not worth the effort unless there is a critical bug that concerns your specific analysis AND Alex Dobin by personal email will n…
Comment: STAR aligner - Is this still maintained? by lieven.sterck 15k
I'm with Rob on that option 4 :) Moreover I would , to some extend, also vote against option 1, mainly given your lack in C/C++ and conse…
Answer: Annotate GWAS result gene function from GFF file by lieven.sterck 15k
If the info you need is available in the GFF file then yes it is possible, however according to GFF specs it is not a necessity to put this…
Comment: STAR aligner - Is this still maintained? by dsull ★ 7.2k
The spam only started about 2-3 weeks ago (during the holidays) by automated spam bots. I think STAR will be ok haha and, yeah, I don't thi…
Comment: drug sensitivity prediction by DareDevil ★ 4.3k
Inputs can be data converted in log2 scale or vst.
Comment: STAR aligner - Is this still maintained? by GenoMax 148k
Every software package reaches a state where it does what most (dare I say 90+%) people want it to do in a stable fashion. So not seeing ne…
Answer: STAR aligner - Is this still maintained? by Rob 7.0k
I think the maintenance frequency has decreased as Alex has moved on to a new job. However, I an my team are working to make several contr…
Comment: drug sensitivity prediction by Luka • 0
Hi, im working with OncoPredict. Can you tell me if you have any info on the input of counts in to the algorithm. Do I need to log transfor…
Comment: b37 liftover by spesks • 0
Thank you! renaming chrs according to hg19 and using hg19 chain files helped.
Comment: Strange offsetting in deeptools? by Elijah ▴ 10
Oh I see! Yes, this is very clear, thank you so much for the in-depth answer :) I think what I was missing was exactly what you said - tha…
Comment: Strange offsetting in deeptools? by rfran010 ★ 1.3k
Yes, the mix up is maybe that your RNA can come from plus or minus strand. Depending on which strand the RNA originated from, Read1 will c…
Comment: Strange offsetting in deeptools? by Elijah ▴ 10
Thank you for your reply! Does filterRNAstrand not remove read 2? From the documentation for filterRNAstrand: "Selects RNA-seq reads (sin…
Comment: Issue with CIBERSORTx Error 139 by jared.andrews07 ★ 18k
I believe the site was down earlier today for a bit as well, so it may have been on their end. They have a banner saying user login is now …
Answer: b37 liftover by Giulio Genovese ▴ 600
Using [BCFtools/liftover](https://doi.org/10.1093/bioinformatics/btae038) will automatically take care of: - flexible contig names (e.g. …
Comment: circos ignoring the ticks and plots by GenoMax 148k
Please copy and paste the actual code instead of posting screenshots. You can format the text as `code` by using `101010` button in edit wi…
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