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2
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3
replies
1.3k
views
How can download and read BAM and FASTQ format
fastq miseq BAM
updated 4.2 years ago by 15k • written 4.2 years ago by • 0
1
vote
3
replies
2.2k
views
log2 normalization produces NaNs
r
updated 2.7 years ago by 45k • written 4.2 years ago by ▴ 70
0
votes
1
reply
1.2k
views
RnBeads Greedycut command ???
greedycut rnbeads array methylation
updated 4.2 years ago by • 0 • written 4.9 years ago by ▴ 520
0
votes
3
replies
1.1k
views
Phylogeny Analysis tools
Phylogeny
updated 4.2 years ago by ★ 2.9k • written 4.2 years ago by ▴ 20
0
votes
3
replies
1.1k
views
how can I get alignment quality from bam index file?
NGS samtools galaxy
updated 2.2 years ago by 45k • written 4.2 years ago by ▴ 30
2
votes
5
replies
1.8k
views
Issue installing Plink
Plink
4.2 years ago by AndrMod • 0
3
votes
2
replies
1.0k
views
Suggestions for an undergraduate research project on glioblastoma
glioblastoma Python Cancer R
updated 4.1 years ago by 45k • written 4.2 years ago by ▴ 100
7
votes
7
replies
9.8k
views
Mummer To Viewable Alignment Format (Fasta Or Aln...)
genomics alignment
updated 4.2 years ago by • 0 • written 14.0 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 2.4 years ago by 45k • written 4.2 years ago by ▴ 170
0
votes
0
replies
592
views
miRNA to families
python families RNAseq miRNA R
4.2 years ago by ehruan ▴ 10
2
votes
7
replies
2.3k
views
Good QC Package (RSeQC or alternative) for Salmon mapping/quantification results?
RSeQC Salmon RNA-Seq mapping
updated 4 months ago by • 0 • written 4.2 years ago by ▴ 80
3
votes
0
replies
3.4k
views
Why does the Seurat FindMarkers function report different log fold change values than the FoldChange function?
single scRNA-seq cell RNA-Seq Seurat
4.2 years ago by imdoingascience ▴ 40
0
votes
1
reply
1.9k
views
High levels of duplicated reads Illumina from PCR-free libraries
fastqc PCR duplicate reads Illumina
updated 4.2 years ago by 153k • written 4.2 years ago by ▴ 40
12
votes
5
replies
1.6k
views
how to sort the rows of a file as a matrix?
linux
updated 23 months ago by 45k • written 4.2 years ago by • 0
2
votes
2
replies
1.8k
views
WGCNA - GTEx RNASeq - Help choosing a soft power
WGCNA RNA-Seq GTEx
4.2 years ago by Branden • 0
0
votes
0
replies
448
views
How to deal with fractional number for enrichment analysis
protein analysis enrichment
4.2 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
4.2 years ago by ConfusedSheep ▴ 10
1
vote
4
replies
2.4k
views
How to view if a gene is protein-coding?
genetics protein-coding genes
updated 4.2 years ago by ★ 1.7k • written 4.2 years ago by ▴ 20
2
votes
6
replies
2.0k
views
IMPUTE2 minimal number of SNPs per chunk
impute gwas
updated 4.2 years ago by 4.8k • written 4.2 years ago by ▴ 420
0
votes
1
reply
893
views
IMPUTE2 limit to only one population of 1000G Reference
GWAS impute 1000g
updated 4.2 years ago by 4.8k • written 4.2 years ago by ▴ 420
1
vote
3
replies
1.4k
views
SortSam Error after BWA alignment
alignment mappingquality picard sortsam bwa
4.1 years ago by loy_loy ▴ 10
2
votes
12
replies
7.4k
views
Confused with 2 SRA runs for one sample
runs Illumina RNASeq sra
4.2 years ago by ConfusedSheep ▴ 10
0
votes
2
replies
1.5k
views
Unicycler error not enough memory available
assembly unicycler memory
updated 4.2 years ago by ★ 29k • written 4.2 years ago by ▴ 170
0
votes
3
replies
4.2k
views
PubChem CID in ChEMBL
ChEMBL PubChem
updated 4.2 years ago by • 0 • written 6.4 years ago by • 0
0
votes
2
replies
893
views
DESeq2 no replicates analysis with a design value of ~1 generates only positive log2foldchange
DESeq2 Log2FoldChange
4.2 years ago by BIN • 0
0
votes
6
replies
1.7k
views
extracting only one sex from gnomad genome v.3.1 file
gnomad
4.2 years ago by storm1907 ▴ 30
4
votes
0
replies
876
views
Herald: The Biostar Herald for Friday, July 02, 2021
herald
updated 4.2 years ago by 20 • written 4.2 years ago by 3.6k
1
vote
7
replies
16k
views
hisat2-align exited with value 1
alignment RNA-Seq rna-seq
updated 4.2 years ago by • 0 • written 6.5 years ago by • 0
1
vote
4
replies
1.2k
views
Pseudocode for gapped BLAST seed extension
Pseudocode smith-waterman seed extend BLAST
updated 4.2 years ago by 153k • written 4.2 years ago by ▴ 10
6
votes
4
replies
1.5k
views
RNA-seq normalisation
normalisation RNAseq
4.2 years ago by raavi21198 ▴ 20
0
votes
0
replies
488
views
Calculate of Total Hip BMD
Hip BMD
4.2 years ago by Yong ▴ 10
1
vote
1
reply
893
views
Identify the potential TF involved in the regulation of DEGs
Transcription factors gene list R
updated 4.2 years ago by ★ 2.2k • written 4.2 years ago by ▴ 30
0
votes
0
replies
740
views
Job: Postdoctoral Associate in statistical geneticist . Nantes/France
france nantes postdoc
4.2 years ago by Pierre Lindenbaum 166k
0
votes
1
reply
965
views
Rarefy metagenomic adatasets for taxonomic profiling using MetaPhlAn3
metagenomics Rarefy MetaPhaln3 Genomics
updated 4.2 years ago by 3.9k • written 4.2 years ago by • 0
1
vote
3
replies
1.2k
views
Calculates the percent sequenceCalculates the percent sequence identity for a pairwise sequence alignment
pairwise sequence alignment identity
updated 3.7 years ago by 23k • written 4.2 years ago by ▴ 20
0
votes
1
reply
924
views
High-throughput sequence variant analysis: Using BAM or VCF files?
ICGC VCF BAM High-throughput
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 110
2
votes
4
replies
1.7k
views
Subsetting fastq file based on reads starting with a specific pattern
fastq subset
4.2 years ago by biomon ▴ 60
2
votes
5
replies
3.0k
views
Visualizing the gene network obtained by WGCNA
WGCNA weighted network visualizing
4.2 years ago by seta ★ 1.9k
4
votes
7
replies
4.2k
views
How to move the files from sub folder and sub-sub folders into one other folder?
bash
updated 2.4 years ago by 45k • written 4.2 years ago by ▴ 80
0
votes
0
replies
946
views
Where to find GATK4 ACNV
segmentation CNV ABSOLUTE GATK
4.2 years ago by noona • 0
3
votes
5
replies
1.6k
views
Integration of two TCGA datasets
r RNA-Seq tcga survival
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 90
3
votes
4
replies
2.1k
views
Generating Positional List from VCF
guidance
updated 22 months ago by ▴ 340 • written 4.2 years ago by ▴ 60
3
votes
6
replies
2.2k
views
KentUtils Installation Problem
kenutils gff3ToGenePred gff3 UCSC gff
4.2 years ago by mglasena ▴ 40
3
votes
3
replies
2.5k
views
DESeq2 saying that dimensions of count matrix and metadata don't agree, but they do agree
expression R differential
4.2 years ago by hippo ▴ 10
7
votes
8
replies
6.3k
views
Aligning PacBio hifiasm CCS to reference genome using pbmm2
assembly pbmm2 pacbio hifiasm
updated 3.4 years ago by ▴ 410 • written 4.3 years ago by ▴ 10
4
votes
6
replies
2.2k
views
How to find out TFBS motifs within 5'-UTR sequences
5prime-UTR TFBSmotifs
updated 13 months ago by 45k • written 4.2 years ago by ▴ 10
1
vote
1
reply
795
views
Ways to mapping a transcriptome against a single gene
annotation RNAseq
updated 4.2 years ago by ★ 7.6k • written 4.2 years ago by ▴ 20
3
votes
3
replies
6.0k
views
How to plot phylogenetic tree using R packages
ape phylogenetic ggtree
4.2 years ago by Kumar ▴ 170
1
vote
3
replies
1.4k
views
Identify unique genes and protein families from eukaryotic genome
Phylogenetic SNP Unique tree gene
updated 4.2 years ago by ★ 2.9k • written 4.2 years ago by ▴ 20
11
votes
13
replies
2.8k
views
6 follow
Bioinformatics
tag1 tag2
updated 4.2 years ago by 22k • written 4.2 years ago by ▴ 30
121,800 results • Page 618 of 2436
Recent Votes
Answer: How to obtain a refFlat file for the Rat
Answer: mummer4: how do I get the mapview executable?
Comment: RTG (Real Time Genomics) docker image - Problem dealing with different VCFs
Answer: GSEA vs GO enrichment
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
A: fgsea: What does fgseaMultilevel argument sampleSize mean/when to change it?
A: fgsea: What does fgseaMultilevel argument sampleSize mean/when to change it?
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Recent Replies
Answer: Local Synteny Analysis with Uncharacterized Genes by Philipp Bayer 8.8k
For gene clusters of this smaller size I'd recommend [clinker](https://github.com/gamcil/clinker) There are some nice automated visualisat…
Comment: Samtools flagstat by Istvan Albert 103k
It is an interesting point that I have not considered. I looked up the SAM specification, it states: For secondary alignments: "*One of …
Comment: Local Synteny Analysis with Uncharacterized Genes by GenoMax 153k
Prior thread with some tools: https://www.biostars.org/p/9477510/ `SynTracker` described in: https://www.nature.com/articles/s41587-024-02…
Comment: mummer4: how do I get the mapview executable? by GenoMax 153k
As long as the output is in the right format mapview should work with v.4.x. You will need to compile it from older release.
Comment: How to detect divergent domains in AlphaFold models (CDD/InterProscan not workin by LLG • 0
Thank you very much, I'll try those!
Comment: mummer4: how do I get the mapview executable? by Tospohh ▴ 10
oh, good catch, I didn't see that. That's a shame. The output in the examples looks very useful. Since there isn't any detail about the rea…
Answer: mummer4: how do I get the mapview executable? by GenoMax 153k
`mapview` program is deemed obsolete in v.4.x (see https://github.com/mummer4/mummer/blob/master/OBSOLETE.md ). You may need to compile it …
Comment: How to obtain a refFlat file for the Rat by GenoMax 153k
> but nothing work What does not work? Once you export a file from the link included, it is in refFlat format.
Comment: RTG (Real Time Genomics) docker image - Problem dealing with different VCFs by stuckinanendlessfebruary • 0
Thanks for replying! Yes, the DRAGEN VCF (dragen_HG008.norm.vcf.gz) is indeed multi-sample, containing both HG008-N (Normal) and HG008-T-m…
Comment: RTG (Real Time Genomics) docker image - Problem dealing with different VCFs by Jeremy Leipzig 23k
which columns are giving you trouble? is the problem that you have two samples in dragen (tumor/normal) and only one sample in the hg008?
Comment: How to obtain a refFlat file for the Rat by AIMAR ▴ 70
I've try the mentioned methods but nothing work that's why I've asked again If I can find a new solution. Thanks !
Answer: How to obtain a refFlat file for the Rat by GenoMax 153k
Please don't ask the same question again in a new thread. This was answered a few weeks back: https://www.biostars.org/p/9613666/#9613671 …
Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful? by benformatics 4.1k
Usually it is not very useful. The only situation where it makes sense to use is where you do a gradient treatment (e.g. 0M, 5M, 50M, et…
Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful? by ATpoint 89k
No, don't rely on numbers. This can and is strongly influences by the sample size and noise, and by this power. Even at same sample size it…
Comment: Pseudobulk analysis using AggregateExpression() by adhisadi • 0
Hi, Did you figure this out? In my data some gene expressed in very low number of cells (less than 1% of total cells) appear as differentia…
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