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687 results • Page 2 of 14
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4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
21 days ago by anna ▴ 20
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN DNA methylation Funnorm
updated 23 days ago by 43k • written 2.4 years ago by ▴ 10
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML ncbi entrez-direct
updated 4 days ago by 43k • written 3.9 years ago by • 0
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 15 days ago by ▴ 10 • written 2.0 years ago by • 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR statistical test parametric non-parametric
updated 17 days ago by ▴ 210 • written 3.9 years ago by ▴ 40
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing coverage
5 days ago by Arton ▴ 10
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring SCTransform Seurat
updated 11 days ago by • 0 • written 2.3 years ago by ▴ 10
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 16 days ago by ★ 7.2k • written 5 months ago by ▴ 10
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 12 days ago by • 0 • written 5.8 years ago by ▴ 30
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq cellranger
updated 1 day ago by ▴ 30 • written 8 months ago by ▴ 870
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 21 days ago by ★ 7.2k • written 8 months ago by ▴ 10
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython FASTA
updated 6 days ago by • 0 • written 2.6 years ago by • 0
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 12 days ago by ▴ 10 • written 2.5 years ago by • 0
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 24 days ago by ★ 2.5k • written 10 weeks ago by • 0
1
vote
2
replies
1.2k
views
News: The GDC Legacy Archive is retiring soon.
genomic-data-commons tcga gdc
15 days ago by Zhenyu Zhang ★ 1.2k
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado filtering QC nanopore Guppy
18 days ago by eebloom ▴ 80
3
votes
0
replies
1.1k
views
Tool: Sars-Cov-2 Genome & ACE 2 Exploration
sequence alignment SNP genome
15 days ago by Ibrahim Tanyalcin ★ 1.2k
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature HGVS
updated 5 hours ago by 43k • written 5 months ago by 4.2k
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
26 days ago by DKA ▴ 40
2
votes
11
replies
1.0k
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 21 days ago by ★ 1.2k • written 4 weeks ago by • 0
2
votes
3
replies
1.0k
views
Method to detect genome doubling
CNV genome doubling
updated 28 days ago by 4.2k • written 4.5 years ago by ▴ 750
13
votes
14
replies
991
views
High Malat-1 expression in single cell data
single-cell
updated 12 days ago by ▴ 40 • written 21 days ago by ▴ 40
7
votes
16
replies
983
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
21 days ago by Ruqaiya • 0
1
vote
8
replies
966
views
Adding CB tag to bam file
samtools bam
updated 25 days ago by 161k • written 4 weeks ago by • 0
2
votes
5
replies
961
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 21 days ago by ★ 2.0k • written 2.1 years ago by • 0
2
votes
9
replies
953
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 26 days ago by 4.2k • written 7 months ago by • 0
4
votes
11
replies
905
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 26 days ago by 4.2k • written 27 days ago by • 0
1
vote
10
replies
903
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 14 days ago by • 0 • written 4 months ago by ▴ 30
0
votes
2
replies
868
views
AGeNT LocatIt
AGeNT LocatIt WES UMI duplicates
updated 26 days ago by ★ 2.2k • written 2.8 years ago by ▴ 10
2
votes
3
replies
858
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 16 days ago by • 0 • written 7 months ago by • 0
10
votes
14
replies
827
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 13 days ago by 142k • written 19 days ago by • 0
4
votes
6
replies
818
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 23 days ago by ★ 6.0k • written 27 days ago by ▴ 10
1
vote
5
replies
811
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator IGV
written 6 months ago by ▴ 30
0
votes
1
reply
806
views
cnetplot category names are too long
clusterprofiler RNA-Seq enrichplot cnetplot
updated 18 days ago by 43k • written 2.7 years ago by • 0
1
vote
3
replies
806
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon chromosome polish genome draft
updated 4 days ago by ▴ 90 • written 2.7 years ago by ▴ 80
0
votes
1
reply
787
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq R cellassign batch-effect
updated 22 days ago by ▴ 10 • written 3.4 years ago by ▴ 30
0
votes
3
replies
778
views
Why cd-hit-est not work when sequence identity threshold<0.95？
genome cluster sequence
updated 20 days ago by • 0 • written 21 months ago by • 0
4
votes
8
replies
775
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 23 days ago by 35k • written 24 days ago by ▴ 10
8
votes
8
replies
774
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 25 days ago by 14k • written 26 days ago by ▴ 10
3
votes
6
replies
769
views
Ciriquant not configuring hisat2 indexed files
ciriquant
28 days ago by Atul K. • 0
3
votes
4
replies
764
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
28 days ago by rahu • 0
3
votes
3
replies
760
views
KissDE and batch effect
kissDE kissplice
28 days ago by david.b.rombaut ▴ 10
1
vote
6
replies
757
views
anRichment is missing
WGCNA anRichment
updated 14 days ago by 142k • written 6 months ago by ▴ 180
0
votes
2
replies
756
views
homer not configured properly
Homer makeTagDirectory
updated 17 days ago by • 0 • written 24 months ago by • 0
1
vote
16
replies
756
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast ncbi
updated 2 days ago by 142k • written 5 days ago by • 0
2
votes
9
replies
756
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 5 days ago by 161k • written 13 days ago by • 0
2
votes
11
replies
738
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio DEG limma
3 days ago by egascon • 0
3
votes
8
replies
734
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 14 days ago by ▴ 410 • written 18 days ago by ▴ 100
5
votes
4
replies
734
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
26 days ago by kirillkirilenko ▴ 40
0
votes
11
replies
731
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
24 days ago by atowns21 • 0
687 results • Page 2 of 14
Recent Votes
Answer: Kraken2 database
A: Why gene expression data should be log2 transformed?
Answer: Filter Genome for Specific Sites
Answer: Filter Genome for Specific Sites
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
The Biostar Herald for Monday, May 20, 2024
Answer: Generating Group/Cluster Lists from fastq files
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Recent Replies
Comment: Trimming tool by Ram 43k
Please do a few simple Google searches before asking others for help.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award by Ram 43k
This post does not fit the theme of this forum.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award by Ram 43k
Hi, Congratulations but this is not LinkedIn, we are not a place to showcase your professional accomplishments. This does not fall under t…
Comment: Kraken2 Custom Database non-deterministic results by GenoMax 142k
Many (most?) programs related to NGS data analysis produce non-deterministic output (unless they explicitly offer an option to produce dete…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl by GenoMax 142k
For those samples it appears that raw data was not submitted. Just an assembly. $ esearch -db biosample -query SAMN08009548 | elink -…
Comment: How can I calculate the OS of each patient? by Pedro • 0
**I have already tried this code. listSamples with HNSC cancer and smokers. I need at least one supporting material to find out the survi…
Comment: Filter Genome for Specific Sites by Anita • 0
Great, thank you!
Comment: Filter Genome for Specific Sites by Anita • 0
This is unhelpful and doesn't answer my question.
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl by Harshita • 0
It seems that the authors in this paper have used paired-end sequences only for their analysis, and for that, they would also have used the…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl by Harshita • 0
Thank you so much for helping me out in this! I have used most of the sequences that are found in this table. But, some samples like the…
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl by GenoMax 142k
Looks like the samples are from this project: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320483&o=acc_s%3Aa This table has the SR…
Comment: Filter Genome for Specific Sites by Pierre Lindenbaum 161k
> My sites are in an Excel file right now ![enter image description here][1] <!-- was an American educator and academic administrator…
Answer: Filter Genome for Specific Sites by GenoMax 142k
> I have a list of ~1,300 single bp sites Convert your file to plain text [**BED format**][1] (three fields required). Use `bedtools slo…
Comment: How to generate an Upset plot in R to plot the shared variants between cell free by sainavyav22 • 0
It worked, Thank you very much!
Comment: What marks a De-Novo Genome assembly as FAILED? by dthorbur ★ 2.0k
I'm unsure you'll be able to identify whole chromosomes that are not core from illumina reads alone. That might be easier to do with a micr…
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