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121,800 results • Page 423 of 2436
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no read counts per allele while using gatk ASEReadCounter
GATK
3.3 years ago by Sara ▴ 280
1
vote
4
replies
1.5k
views
how to link hmmalign result and FastTree or other Tree tools
FastTree hmmalign Phylogenetic_tree
3.3 years ago by shangguandong1996 ▴ 30
0
votes
1
reply
824
views
Distribution of annotated genomic regions in DNAm probes using UCSC_RefGene_Group
DNA EPIC R methylation
updated 3.2 years ago by ▴ 10 • written 3.3 years ago by • 0
3
votes
6
replies
2.0k
views
Help with PCA plot from SNPRelate
PLOT SNPRelate PCA
updated 3.3 years ago by 153k • written 3.3 years ago by • 0
0
votes
0
replies
462
views
WGCNA consensus between RNA seq and microarray datasets
RNA-seq microarray WGCNA
3.3 years ago by Harrsha • 0
4
votes
2
replies
2.6k
views
correct list of capture targets/intervals for SureSelect mouse exome to perform GATK Mutect2
mouse exom Mutect2 list of intervals pon
updated 3.3 years ago by ▴ 110 • written 5.8 years ago by ▴ 40
0
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1
reply
2.0k
views
Infinium MethylationEPIC Annotation under hg38
Microarray Methylation
3.3 years ago by Molin ▴ 10
1
vote
1
reply
1.6k
views
Illumina EPIC array manifest file header
EPICarray Illumina
updated 3.3 years ago by ▴ 10 • written 3.6 years ago by • 0
0
votes
2
replies
1.3k
views
Third Quartile (Q3) for RNAseq data
normalization RNAseq Third Q3 R
3.3 years ago by Leo • 0
1
vote
2
replies
2.0k
views
Admixture: "PLINK Input file error"
plink admixture
3.2 years ago by dec986 ▴ 380
0
votes
0
replies
889
views
Job: Staff Data Scientist, Computational Biology
learning immunology cardiovascular drug machine biology discovery Computational
3.3 years ago by arajan • 0
2
votes
2
replies
816
views
Build canine dna.primary_assembly.fa for kb ref
bustools Ensembl kallisto
updated 2.2 years ago by 45k • written 3.3 years ago by • 0
1
vote
2
replies
2.4k
views
What is Nanopore Barcode Score and how is it calculated?
barcoding nanopore demultiplexing DNA-Seq
updated 3.3 years ago by 3.9k • written 3.5 years ago by ▴ 10
0
votes
0
replies
455
views
Standard for aligning smallRNA to a reference human rRNA?
rRNA RNAseq miRNA
3.3 years ago by Mauro ▴ 20
0
votes
0
replies
562
views
Help with mounting VCF file parameters adenovo
denovo stacks snp vcf asembly
3.3 years ago by Pamella • 0
2
votes
5
replies
2.5k
views
Giotto Error: py_run_file_impl(file, local, convert) : ModuleNotFoundError: No module named 'dataclasses'
Giotto ModuleNotFoundError
3.2 years ago by Agatha Nabilla L ▴ 10
4
votes
4
replies
1.4k
views
Renaming reads
fastq rename sed UMI
3.2 years ago by vvs.hazia ▴ 10
0
votes
2
replies
1.3k
views
User error in GATK CreateSomaticPanelOfNormals
gatk CreateSomaticPanelOfNormals user-error
3.2 years ago by Hasib ▴ 20
0
votes
0
replies
443
views
Drawing multiple genes and adding possibile functional sites (from Clover)?
gviz ensembl r clover biomart
3.3 years ago by Ale • 0
11
votes
8
replies
12k
views
7 follow
Working with GTEX dataset
GTEX RNA-Seq
updated 2.7 years ago by 45k • written 10.2 years ago by ▴ 150
0
votes
1
reply
905
views
Integrate scRNAseq with 10x Multiome
10x Multiome
updated 3.3 years ago by ▴ 50 • written 3.3 years ago by ▴ 10
1
vote
1
reply
789
views
Looking for Bulk RNA seq PBMC data
rba genome rna-seq
updated 3.2 years ago by 45k • written 3.3 years ago by ▴ 70
0
votes
4
replies
1.3k
views
FASTA sequence retrieval
FASTA Genes DEGs
3.2 years ago by Roy.anupama11 • 0
0
votes
1
reply
3.1k
views
How to use NCBI API key for Entrez (Biopython)?
NCBI Entrez
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by • 0
5
votes
5
replies
14k
views
How to get number of characters (nucleotides) in fasta file
count fasta linux characters commands
updated 3.3 years ago by • 0 • written 4.2 years ago by ▴ 30
2
votes
4
replies
1.6k
views
Htseq-count: Problem with feature counts
gtf RNA-Seq htseq-count
updated 3.3 years ago by 103k • written 3.3 years ago by ▴ 80
0
votes
1
reply
584
views
identification of agilent micro array non coding RNA id
micro id conversion array
updated 3.3 years ago by 153k • written 3.3 years ago by • 0
10
votes
10
replies
4.2k
views
6 follow
Rna Seq Analysis Script
Next-Gen-Sequencing Script Ubuntu bash RNA-Seq
3.3 years ago by SomeOne ▴ 240
0
votes
0
replies
953
views
Job: ML researcher - Oxford-GSK Institute for Molecular and Computational Medicine (IMCM) in data analysis and integration in neurodegenerative disease
learning integration Machine IMCM neurodegeneration analysis
3.3 years ago by SH01 • 0
1
vote
1
reply
1.2k
views
Gene enrichment analysis R studio error
RStudio
updated 3.3 years ago by ▴ 10 • written 3.6 years ago by • 0
0
votes
1
reply
562
views
Morbidity inheritance dataset
inheritance Morbidity
updated 3.3 years ago by 56k • written 3.3 years ago by ▴ 110
1
vote
1
reply
875
views
What is a biologically meaningful size of gene module?
module gene
updated 3.3 years ago by 3.9k • written 3.3 years ago by ▴ 60
0
votes
0
replies
488
views
Immediate segmentation error when using STAR on SMART-Seq data
segmentation smart-seq dumped scRNA-seq STAR
3.3 years ago by Bertalan_Takacs ▴ 140
0
votes
1
reply
719
views
Genome Fasta and compatible tss region database
igv tss fasta tata box
updated 3.3 years ago by ★ 3.0k • written 3.3 years ago by • 0
0
votes
2
replies
976
views
bwa error
index bwa
updated 2.4 years ago by 45k • written 3.3 years ago by • 0
2
votes
2
replies
1.0k
views
CNV analysis
DELLY CNV wholegenomesequencing S.pombe
3.3 years ago by archanaverma433 ▴ 10
0
votes
2
replies
871
views
Can a pathogenic mutation results in the up-regulation of a gene?
mutation-up-regulation Pathogenic
3.3 years ago by nazaninhoseinkhan ▴ 530
0
votes
3
replies
1.4k
views
DESeq2 use of factors for colData
DESeq2 expression differential
updated 3.3 years ago by 15k • written 3.3 years ago by ▴ 30
2
votes
2
replies
1.2k
views
How to provide read1 and read2 fastq files from two lanes to kallisto | bustools?
kallisto 10X bustools scRNA-seq
3.3 years ago by eager_underdog • 0
11
votes
5
replies
9.4k
views
6 follow
How to make a summary plot like below?
cancer classes Oncoplots
updated 3.3 years ago by ▴ 340 • written 4.2 years ago by ▴ 10
3
votes
4
replies
1.7k
views
snakemake r script
pipeline snakemake
3.3 years ago by nishimalhotra2612 ▴ 50
0
votes
10
replies
2.6k
views
Reassembly after Binning
binning
3.2 years ago by Tanker • 0
0
votes
0
replies
529
views
extract utr 5' from refGene.txt
genes utr igv
3.3 years ago by Luca • 0
1
vote
8
replies
2.6k
views
AttributeError: 'int' object has no attribute 'seq'
BioPython AttributeError
3.2 years ago by Robert • 0
6
votes
6
replies
7.2k
views
How to remove rRNA, bacterial RNA and polyA contamination from RNA-seq data(fastq format)?
RNA-Seq sequencing
updated 3.3 years ago by ▴ 40 • written 8.2 years ago by ▴ 50
19
votes
8
replies
23k
views
7 follow
rRNA Removal In Rna-Seq Data
rna-seq deseq
updated 2.7 years ago by ▴ 10 • written 11.8 years ago by ▴ 440
29
votes
18
replies
28k
views
9 follow
Cleaning RNA-Seq data from rRNA
RNA-Seq rRNA cleaning QC
updated 3.3 years ago by ▴ 40 • written 9.4 years ago by ▴ 270
16
votes
7
replies
8.3k
views
6 follow
rRNA decontamination of RNA-Seq reads (tool choice, introns etc)
rRNA intron RNA-Seq bbsuite sormeRNA
updated 2.5 years ago by 153k • written 5.8 years ago by ▴ 640
8
votes
10
replies
10k
views
8 follow
rRNA remove from RNAseq data
RNA-Seq
updated 3.3 years ago by ▴ 40 • written 7.1 years ago by ▴ 40
1
vote
4
replies
1.2k
views
Tool: Quick Command to Filter Bam Files
bed awk
3.3 years ago by Sasha ▴ 850
121,800 results • Page 423 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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