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86 results • Page
2 of 2
Sort: Votes
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0
votes
1
reply
113
views
How to process Bulk WES data?
WES
WGS
updated 16 hours ago by
GenoMax
142k • written 17 hours ago by
wyuan37
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 15 hours ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
0
votes
1
reply
113
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 15 hours ago by
GenoMax
142k • written 18 hours ago by
cedric.blais
• 0
0
votes
0
replies
64
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
10 hours ago by
Holly
• 0
0
votes
0
replies
176
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
10 hours ago by
Emily
▴ 20
0
votes
3
replies
276
views
Snakemake wrapper issue
fastqc
snakemake
updated 9 hours ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
47
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
8 hours ago by
Spring
• 0
0
votes
2
replies
106
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
5 hours ago by
IdaHao0921
• 0
0
votes
4
replies
185
views
Galaxy StringTie error
stringtie
galaxy
4 hours ago by
trkfs
• 0
0
votes
3
replies
87
views
How to access GWAVA software of data
GWAVA
updated 1 hour ago by
GenoMax
142k • written 4 hours ago by
nonaddldy
▴ 10
0
votes
0
replies
17
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 1 hour ago by
GenoMax
142k • written 1 hour ago by
Bhavya
• 0
0
votes
1
reply
31
views
sci-RNA-seq
sci-RNA-seq
clusters
combinatorial
single
updated 46 minutes ago by
ATpoint
82k • written 1 hour ago by
kilcdincer
▴ 10
0
votes
1
reply
253
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Sony
▴ 10
0
votes
0
replies
14
views
Is there a real ground truth for CNV data?
CNV
28 minutes ago by
jennyp0706
• 0
0
votes
2
replies
262
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
6 days ago by
sainavyav22
• 0
0
votes
0
replies
97
views
monocle 3-- Could not get node in small cluster
monocle3
6 days ago by
synat.keam
▴ 100
0
votes
0
replies
104
views
meffil.snp.concordance
meffil
methylation
snp_concordance
6 days ago by
kyj222637
• 0
0
votes
0
replies
119
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
6 days ago by
Omics data mining
▴ 260
0
votes
0
replies
142
views
Chance for trained without experience
bio
updated 6 days ago by
ATpoint
82k • written 6 days ago by
shehab
• 0
0
votes
2
replies
179
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
6 days ago by
njornet
▴ 20
0
votes
5
replies
255
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 6 days ago by
Joe
21k • written 6 days ago by
Lemonhope
• 0
0
votes
1
reply
151
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 5 days ago by
Bastien Hervé
5.3k • written 6 days ago by
sooni
▴ 20
0
votes
2
replies
205
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
5 days ago by
Nicholas
• 0
0
votes
2
replies
205
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 5 days ago by
Adam
▴ 30 • written 6 days ago by
Darya
• 0
0
votes
2
replies
218
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 5 days ago by
swbarnes2
14k • written 7 days ago by
ahmad.sajad4541
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 5 days ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
0
votes
0
replies
103
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 5 days ago by
Ram
43k • written 5 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
115
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
5 days ago by
asalimih
▴ 60
0
votes
0
replies
113
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 5 days ago by
Ram
43k • written 5 days ago by
curious_butterfly
• 0
0
votes
0
replies
174
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
5 days ago by
Winter
• 0
0
votes
0
replies
106
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
5 days ago by
Javier
• 0
0
votes
0
replies
180
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
4 days ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
144
views
input file for alternative splicing in rmats in linux
rmats
updated 4 days ago by
Ram
43k • written 5 days ago by
Lambodarswain316
• 0
0
votes
0
replies
154
views
supervised admixture
supervised
admixture
4 days ago by
RT
▴ 10
0
votes
0
replies
147
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
4 days ago by
Aytaç
• 0
0
votes
0
replies
137
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
4 days ago by
singcell
• 0
86 results • Page
2 of 2
Recent Votes
C: What % of rRNA contamination is acceptable?
A: What % of rRNA contamination is acceptable?
A: GC bias correction for Chip-SEQ
Comment: Help with IGV abbreviation
A: How to get read counts on transcript level using featurecounts?
Answer: Vcf file sorting
Answer: How to interpret infinite odds ratio?
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Recent Replies
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
by
J.
▴ 10
FYI if you also have this problem, this seems to be a pretty good solution: https://github.com/harvardinformatics/degenotate
Comment: Biomart issue, why so few 3'utrs?
by
GenoMax
142k
AFAIK "MANE" project is only for human protein-coding genes. One potential explanation. Out of the 2000 ID's only 125 may be MANE. https:…
Answer: Biomart issue, why so few 3'utrs?
by
i.sudbery
19k
The MANE-select transcripts are pairs of identically annotated transcripts in ReqSeq and Ensembl. The 3' UTR is the region where otherwise …
Comment: sci-RNA-seq
by
ATpoint
82k
Please understand that this impossibly can be answered without any code or plots, or details in general. "Hey my car does not start, it mak…
Comment: Biomart issue, why so few 3'utrs?
by
i.sudbery
19k
Which species is this?
Comment: How to access GWAVA software of data
by
GenoMax
142k
Please email the author (grsr at ebi.ac.uk) and let them know that the link above is not available.
Comment: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Answer: Overlapping Ranges within Granges object
by
ATpoint
82k
There is no one-hit function in GenomicRanges, but you can stick something together using a combination of `findOverlaps` to first find ove…
Comment: Galaxy StringTie error
by
trkfs
• 0
Hi, I did not encounter any " \ - " characters in the fastq input files, and it doesn't seem to be present in any other files either. Thank…
Comment: How to interpret infinite odds ratio?
by
Lukas
• 0
Thanks you for your answer. But according that links interpretation of inf odds ratio is up to hypothesis of the researcher.So my solution …
Comment: How to access GWAVA software of data
by
nonaddldy
▴ 10
Not found in https://ftp.sanger.ac.uk/resources/software/gwava/ ![][1] [1]: /media/images/f69695ec-e047-44f6-95ce-cd4edf1c
Comment: How to access GWAVA software of data
by
nonaddldy
▴ 10
https://www.sanger.ac.uk/tool/gwava/
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