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86 results • Page 2 of 2
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77
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat single-cell scRNA-seq
updated 22 hours ago by 43k • written 1 day ago by ▴ 20
0
votes
5
replies
217
views
Why most genes have high padj values
RNA-seq DEG
updated 22 hours ago by 43k • written 1 day ago by • 0
0
votes
2
replies
266
views
How can I calculate the OS of each patient?
overall-survival
20 hours ago by Pedro • 0
0
votes
0
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135
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 19 hours ago by 43k • written 1 day ago by ▴ 20
0
votes
0
replies
117
views
problems in installing rDock
rDock
updated 19 hours ago by 43k • written 2 days ago by • 0
0
votes
3
replies
209
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 18 hours ago by ▴ 130 • written 1 day ago by ▴ 20
0
votes
5
replies
343
views
how to treat the replicates while performing WGCNA
clustering WGCNA replicates
17 hours ago by mavy ▴ 10
0
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0
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57
views
Multi-ploid data in ANGSD and NGSadmix
ancestry diploid haploid admixture
13 hours ago by Christopher • 0
0
votes
1
reply
78
views
Nextflow docker: Error response from daemon
sarek gatk4 docker nextflow
updated 7 hours ago by 161k • written 7 hours ago by ▴ 200
0
votes
0
replies
48
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ single-cell TCR-seq cellranger 10x
7 hours ago by dawnyipingzou • 0
0
votes
0
replies
38
views
Calculated LAI is too large
annotation LAI assembly TE genome
5 hours ago by Yao ▴ 30
0
votes
1
reply
100
views
vcf phasing
beagle WhatsHap phasing
updated 2 hours ago by 47k • written 1 day ago by ▴ 10
0
votes
1
reply
81
views
CreateSeuratObject taking very long
seurat
updated 2 hours ago by ★ 1.6k • written 11 hours ago by • 0
0
votes
0
replies
18
views
Last step of metagenome analysis before visualization
metagenome python analyis
1 hour ago by Ayda Ecem • 0
0
votes
2
replies
85
views
Where to find old version of GATK best practice
gatk
updated 1 hour ago by 142k • written 7 hours ago by ★ 1.2k
0
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3
replies
56
views
Generating a Bed file from a Fasta file
bedfile Sequences Random NullSeq
updated 1 hour ago by 161k • written 2 hours ago by • 0
0
votes
2
replies
126
views
Kraken2 Custom Database non-deterministic results
Metagenomics kraken2
1 hour ago by Bjorn • 0
0
votes
0
replies
14
views
converting transcript IDs (Ensembl) to gene symbols in R
RNAseq
44 minutes ago by ashkan ▴ 160
0
votes
1
reply
25
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN GenomicsDB
updated 41 minutes ago by ▴ 300 • written 1 hour ago by • 0
0
votes
1
reply
21
views
z-score of gene set
z-score scRNA set gene
updated 10 minutes ago by ★ 2.5k • written 59 minutes ago by • 0
0
votes
0
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3
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast vcf identification gene fasta
1 minute ago by Harshita • 0
0
votes
0
replies
99
views
NEURON, Brian2, NEST, or PyNN
NEST NEURON PyNN Brian2
6 days ago by brunofelicianodeomena • 0
0
votes
0
replies
104
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS ggplot2 ggplot R
updated 6 days ago by 142k • written 6 days ago by • 0
0
votes
1
reply
153
views
Polish a large genome with Pilon
Pilon Pacbio Polish Illumina
6 days ago by sansan_96 ▴ 90
0
votes
2
replies
210
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming adapters cutadapt sRNA-seq smallRNA
6 days ago by melissa.joubert • 0
0
votes
0
replies
100
views
ReactomeGSA
ReactomeGSA
6 days ago by Shaimaa Gamal ▴ 10
0
votes
3
replies
181
views
Problem with Calling Variants from RNA-Seq data
vcf gatk benchmark giab rna-seq
6 days ago by Esraa • 0
0
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0
replies
115
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity metatranscriptome
5 days ago by jway • 0
0
votes
1
reply
143
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation vcf vep zygosity deepvariant
5 days ago by asalimih ▴ 60
0
votes
0
replies
115
views
DOCK6 installation on MacOS M1
installation troubleshooting DOCK6
updated 5 days ago by 142k • written 5 days ago by • 0
0
votes
9
replies
617
views
Using VEP annotation output as the input for a second VEP annotation
Annotation VEP VCF
5 days ago by Arton ▴ 10
0
votes
5
replies
299
views
bbmerge (bbmap) ~ error with insert size file output
bbtools bbmerge bbmap
updated 5 days ago by 142k • written 6 days ago by • 0
0
votes
0
replies
150
views
select set of intervals that cover a genomic region
GRanges bed
5 days ago by ntsopoul ▴ 60
0
votes
0
replies
146
views
qPCR gene expression data analysis
qPCR geneexpression anova
5 days ago by ebertomeup • 0
0
votes
1
reply
182
views
What's next after GATK variant calling pipeline?
GATK pipeline figures DNA-seq
updated 5 days ago by 54k • written 5 days ago by ▴ 30
0
votes
1
reply
182
views
perseus software (version 1.5.5)
preseus mass spectrometry data
updated 5 days ago by ▴ 20 • written 6 days ago by • 0
86 results • Page 2 of 2
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Comment: Practical Haplotype Graph v2 not finding correct paths
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How To Convert List Of Entrez Ids Into Gene Name
A: RSeQC Output from infer_experiment.py - what does it mean?
A: findOverlaps function in R
Comment: What marks a De-Novo Genome assembly as FAILED?
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Comment: z-score of gene set by bk11 ★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB by DBScan ▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
Answer: Practical Haplotype Graph v2 not finding correct paths by beantkapoor16 ▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results by Bjorn • 0
Thank you!
Comment: Generating a Bed file from a Fasta file by Pierre Lindenbaum 161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths by beantkapoor16 ▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file by pirku • 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice by GenoMax 142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file by Pierre Lindenbaum 161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
Answer: Running STRUCTURE from command line by Arthur • 0
If it cans help, I got the same error message : There were errors in the input file (listed above). According to "mainparams" the inp…
Comment: CreateSeuratObject taking very long by Nitin Narwade ★ 1.6k
I am not sure whether it will speedup the conversion but you can give it a try. convert your dataframe into a sparse matrix before creatin…
Comment: Practical Haplotype Graph v2 not finding correct paths by pjb39 ▴ 220
The timing for your question is excellent. The fix was released yesterday.
Comment: vcf phasing by WouterDeCoster 47k
> I observed that it doesn't phase genotypes labeled as 0/0 How could such a genotype even be phased?
Comment: Super ehancers by Oburah • 0
Well-noted however just wondering what you me by GFF being shorter. Thank you![See the screeshot snap of the gff file][1] [1]: /media/i…
Comment: What marks a De-Novo Genome assembly as FAILED? by Umer ▴ 50
I know illumina will only give me high-quality contigs. the samples which are to be sequenced with Long_Short read sequence will be used as…
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