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121,994 results • Page 622 of 2440
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1.0k
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Tripal Fancy Fields
tripal
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 120
2
votes
2
replies
1.2k
views
How much would it cost to do a de novo assembly (plus annotation) of a jellifish genome?
novo genome de assembly budgeting
4.1 years ago by ilante ▴ 30
1
vote
3
replies
1.3k
views
how to do make differential expression of lncRNA from RNA-seq data
lncRNA mRNA RNA-seq
updated 4.3 years ago by ★ 2.6k • written 4.3 years ago by ▴ 30
1
vote
3
replies
1.6k
views
Filtering nuclear RNA expression instead of MT expression in Scanpy
filtering nRNA scanpy scRNAseq mtRNA
updated 2.7 years ago by • 0 • written 4.3 years ago by • 0
2
votes
3
replies
1.4k
views
How can download and read BAM and FASTQ format
fastq miseq BAM
updated 4.3 years ago by 15k • written 4.3 years ago by • 0
1
vote
3
replies
2.3k
views
log2 normalization produces NaNs
r
updated 2.8 years ago by 45k • written 4.3 years ago by ▴ 70
0
votes
1
reply
1.3k
views
RnBeads Greedycut command ???
greedycut rnbeads array methylation
updated 4.3 years ago by • 0 • written 5.0 years ago by ▴ 520
0
votes
3
replies
1.2k
views
Phylogeny Analysis tools
Phylogeny
updated 4.3 years ago by ★ 2.9k • written 4.3 years ago by ▴ 20
0
votes
3
replies
1.2k
views
how can I get alignment quality from bam index file?
NGS samtools galaxy
updated 2.3 years ago by 45k • written 4.3 years ago by ▴ 30
2
votes
5
replies
1.9k
views
Issue installing Plink
Plink
4.3 years ago by AndrMod • 0
3
votes
2
replies
1.1k
views
Suggestions for an undergraduate research project on glioblastoma
glioblastoma Python Cancer R
updated 4.2 years ago by 45k • written 4.3 years ago by ▴ 100
7
votes
7
replies
10k
views
Mummer To Viewable Alignment Format (Fasta Or Aln...)
genomics alignment
updated 4.3 years ago by • 0 • written 14.1 years ago by ★ 2.5k
0
votes
0
replies
1.0k
views
how to get effect sizes (R2) in result of GEMMA?
GEMMA SNP
updated 2.5 years ago by 45k • written 4.3 years ago by ▴ 170
0
votes
0
replies
609
views
miRNA to families
python families RNAseq miRNA R
4.3 years ago by ehruan ▴ 10
2
votes
7
replies
2.4k
views
Good QC Package (RSeQC or alternative) for Salmon mapping/quantification results?
RSeQC Salmon RNA-Seq mapping
updated 6 months ago by • 0 • written 4.3 years ago by ▴ 80
3
votes
0
replies
3.5k
views
Why does the Seurat FindMarkers function report different log fold change values than the FoldChange function?
single scRNA-seq cell RNA-Seq Seurat
4.3 years ago by imdoingascience ▴ 40
0
votes
1
reply
2.0k
views
High levels of duplicated reads Illumina from PCR-free libraries
fastqc PCR duplicate reads Illumina
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 40
12
votes
5
replies
1.7k
views
how to sort the rows of a file as a matrix?
linux
updated 2.0 years ago by 45k • written 4.3 years ago by • 0
2
votes
2
replies
1.9k
views
WGCNA - GTEx RNASeq - Help choosing a soft power
WGCNA RNA-Seq GTEx
4.3 years ago by Branden • 0
0
votes
0
replies
468
views
How to deal with fractional number for enrichment analysis
protein analysis enrichment
4.3 years ago by Cancan • 0
0
votes
2
replies
1.9k
views
Normalization/Scaling with sctransform in RStudio of scRNASeq data
vst normalization sctransform scRNASeq scaling
4.3 years ago by ConfusedSheep ▴ 10
1
vote
4
replies
2.5k
views
How to view if a gene is protein-coding?
genetics protein-coding genes
updated 4.3 years ago by ★ 1.7k • written 4.3 years ago by ▴ 20
2
votes
6
replies
2.1k
views
IMPUTE2 minimal number of SNPs per chunk
impute gwas
updated 4.3 years ago by 4.8k • written 4.3 years ago by ▴ 420
0
votes
1
reply
935
views
IMPUTE2 limit to only one population of 1000G Reference
GWAS impute 1000g
updated 4.3 years ago by 4.8k • written 4.3 years ago by ▴ 420
1
vote
3
replies
1.5k
views
SortSam Error after BWA alignment
alignment mappingquality picard sortsam bwa
4.2 years ago by loy_loy ▴ 10
2
votes
12
replies
7.9k
views
Confused with 2 SRA runs for one sample
runs Illumina RNASeq sra
4.3 years ago by ConfusedSheep ▴ 10
0
votes
2
replies
1.5k
views
Unicycler error not enough memory available
assembly unicycler memory
updated 4.3 years ago by ★ 30k • written 4.3 years ago by ▴ 170
0
votes
3
replies
4.5k
views
PubChem CID in ChEMBL
ChEMBL PubChem
updated 4.3 years ago by • 0 • written 6.5 years ago by • 0
0
votes
2
replies
929
views
DESeq2 no replicates analysis with a design value of ~1 generates only positive log2foldchange
DESeq2 Log2FoldChange
4.3 years ago by BIN • 0
0
votes
6
replies
1.7k
views
extracting only one sex from gnomad genome v.3.1 file
gnomad
4.3 years ago by storm1907 ▴ 30
4
votes
0
replies
900
views
Herald: The Biostar Herald for Friday, July 02, 2021
herald
updated 4.3 years ago by 20 • written 4.3 years ago by 3.6k
1
vote
7
replies
16k
views
hisat2-align exited with value 1
alignment RNA-Seq rna-seq
updated 4.3 years ago by • 0 • written 6.6 years ago by • 0
1
vote
4
replies
1.2k
views
Pseudocode for gapped BLAST seed extension
Pseudocode smith-waterman seed extend BLAST
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 10
6
votes
4
replies
1.5k
views
RNA-seq normalisation
normalisation RNAseq
4.3 years ago by raavi21198 ▴ 20
0
votes
0
replies
502
views
Calculate of Total Hip BMD
Hip BMD
4.3 years ago by Yong ▴ 10
1
vote
1
reply
933
views
Identify the potential TF involved in the regulation of DEGs
Transcription factors gene list R
updated 4.3 years ago by ★ 2.2k • written 4.3 years ago by ▴ 30
0
votes
0
replies
756
views
Job: Postdoctoral Associate in statistical geneticist . Nantes/France
france nantes postdoc
4.3 years ago by Pierre Lindenbaum 166k
0
votes
1
reply
1.0k
views
Rarefy metagenomic adatasets for taxonomic profiling using MetaPhlAn3
metagenomics Rarefy MetaPhaln3 Genomics
updated 4.3 years ago by 3.9k • written 4.3 years ago by • 0
1
vote
3
replies
1.3k
views
Calculates the percent sequenceCalculates the percent sequence identity for a pairwise sequence alignment
pairwise sequence alignment identity
updated 3.8 years ago by 23k • written 4.3 years ago by ▴ 20
0
votes
1
reply
967
views
High-throughput sequence variant analysis: Using BAM or VCF files?
ICGC VCF BAM High-throughput
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 110
2
votes
4
replies
1.8k
views
Subsetting fastq file based on reads starting with a specific pattern
fastq subset
4.3 years ago by biomon ▴ 60
2
votes
5
replies
3.1k
views
Visualizing the gene network obtained by WGCNA
WGCNA weighted network visualizing
4.3 years ago by seta ★ 1.9k
4
votes
7
replies
4.3k
views
How to move the files from sub folder and sub-sub folders into one other folder?
bash
updated 2.6 years ago by 45k • written 4.3 years ago by ▴ 80
0
votes
0
replies
975
views
Where to find GATK4 ACNV
segmentation CNV ABSOLUTE GATK
4.3 years ago by noona • 0
3
votes
5
replies
1.7k
views
Integration of two TCGA datasets
r RNA-Seq tcga survival
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 90
3
votes
4
replies
2.2k
views
Generating Positional List from VCF
guidance
updated 24 months ago by ▴ 340 • written 4.3 years ago by ▴ 60
3
votes
6
replies
2.3k
views
KentUtils Installation Problem
kenutils gff3ToGenePred gff3 UCSC gff
4.3 years ago by mglasena ▴ 40
3
votes
3
replies
2.6k
views
DESeq2 saying that dimensions of count matrix and metadata don't agree, but they do agree
expression R differential
4.3 years ago by hippo ▴ 10
7
votes
8
replies
6.7k
views
Aligning PacBio hifiasm CCS to reference genome using pbmm2
assembly pbmm2 pacbio hifiasm
updated 3.5 years ago by ▴ 410 • written 4.4 years ago by ▴ 10
4
votes
6
replies
2.4k
views
How to find out TFBS motifs within 5'-UTR sequences
5prime-UTR TFBSmotifs
updated 14 months ago by 45k • written 4.3 years ago by ▴ 10
121,994 results • Page 622 of 2440
Recent Votes
Answer: SNP calling ONT sequenced files
Answer: SNP calling ONT sequenced files
Answer: Combine a directory of GVCF files with gatk CombineGVCFs
Answer: Combine a directory of GVCF files with gatk CombineGVCFs
A: Trimmomatic Error: Unable to detect quality encoding
A: Trimmomatic Error: Unable to detect quality encoding
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
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Recent Replies
Answer: Transverse data by basu • 0
Sounds like you’ve got a data party going on—too many duplicates crashing it! If you need a quick fix for those pesky repeats, maybe check …
Answer: Pseudogene - scarce info by Mensur Dlakic ★ 30k
> The gene plays a pivotal role in some pathways of the immune response, but tbh I could'nt find any mention of my pseudogene on the linked…
Answer: SNP calling ONT sequenced files by cfos4698 ★ 1.2k
My personal preference is using [clair3][1]. I'm unsure if CLC didn't work because your compute resources are too limited, or if there are …
Comment: HIV NL4-3 transcriptome fasta by Ales ▴ 50
Hi, Wanted to update here that full transcriptome annotations for thousands of hiv genomes (including NL4-3) are now available at https://…
Answer: HIV NL4-3 transcriptome fasta by Ales ▴ 50
You can get full transcriptome annotation for the NL4-3 genomes: https://ccb.jhu.edu/HIV_Atlas/11676/AF324493.2 . Note the accession ID tho…
Answer: Doubt on docking by Mensur Dlakic ★ 30k
I think you are wrongly assuming that we can help you with this without knowing what is the protein of interest. A general answer is that …
Answer: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
The post looks much better now, so you did something. The preview here works fine. It simply can't be that the preview for your original po…
Comment: GUI commercial software for 10x single cell gene expression analysis by GenoMax 154k
Black box software has its cons but in instances like what OP needs that may be the only viable option. Their use limits reproducibility as…
Comment: downloading raw bam files from pacbio sequencer by GenoMax 154k
Have you checked : https://www.pacb.com/connect/datasets/
Comment: TMM-Normalization by kalavattam ▴ 380
No, but a modified version of TMM does: “GeTMM.” See the paper [here](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-0…
Comment: Difficulty running FoldX in linux by strayeroliver • 0
Responding to your answer. - I spent a lot of time formatting it just right, using the ``` methodology you mentioned. It looks very good o…
Comment: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by Phil Ewels ★ 1.5k
Found the docs: https://www.nextflow.io/docs/latest/process.html#multiple-input-files | Arity | Name pattern | Staged file names | |---|--…
Comment: Dorado in PowerShell on Windows by jared.andrews07 ★ 19k
No more than running it on native Linux (as that's what WSL is at this point).
Answer: SNP calling ONT sequenced files by colindaven 8.0k
The quality of (modern, SUP basecalled, but certainly not fast basecalled) ONT sequences should be fine, especially for bacterial SNP call…
Comment: SNP calling ONT sequenced files by GenoMax 154k
What is the median length of raw reads and how many do you have? Has the data been basecalled with "high" or "super" accuracy? > I have …
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