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52 results • Page
1 of 2
Sort: Votes
Rank
Views
Votes
Replies
4
votes
7
replies
379
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
15 hours ago by
Chen
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 5 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
4
votes
1
reply
95
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
1 hour ago by
J.
▴ 40
3
votes
3
replies
315
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 16 hours ago by
Mathew
▴ 140 • written 3 days ago by
Christopher
• 0
3
votes
2
replies
239
views
imputation through beagle
panel
beagle
reference
imputation
8 hours ago by
analyst
▴ 50
3
votes
3
replies
253
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 18 hours ago by
Ram
43k • written 14 days ago by
Adyasha
• 0
2
votes
3
replies
230
views
Finding variants within a subset of a BAM file
variant
calling
2 minutes ago by
ramiro.barrantes
• 0
2
votes
4
replies
269
views
BWA alignment
Samtools
bam
updated 9 hours ago by
ATpoint
82k • written 1 day ago by
Vahid
• 0
2
votes
4
replies
141
views
Help with IGV abbreviation
Genome
browser
15 hours ago by
GeneC
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 5 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
2
votes
5
replies
193
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 12 hours ago by
Philipp Bayer
8.5k • written 16 hours ago by
林明德
• 0
1
vote
2
replies
131
views
Duplicated sequence samtools
bowtie2
samtools
updated 22 hours ago by
GenoMax
142k • written 23 hours ago by
Moinuddin
• 0
1
vote
4
replies
324
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 18 hours ago by
Ram
43k • written 5 days ago by
samRayne
• 0
1
vote
4
replies
368
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 20 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
1
vote
2
replies
167
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 23 hours ago by
lagartija
▴ 160 • written 1 day ago by
Esraa
• 0
1
vote
3
replies
327
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
21 hours ago by
kalavattam
▴ 190
1
vote
3
replies
203
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
8 hours ago by
Vijith
▴ 30
1
vote
1
reply
121
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 8 hours ago by
zx8754
11k • written 15 hours ago by
ohtang7
▴ 40
1
vote
2
replies
203
views
How to interpret infinite odds ratio?
statistics
5 hours ago by
Lukas
• 0
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 16 hours ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
0
votes
1
reply
78
views
What is the bin size for Bamcompare?
bin
chipseq
size
bamcompare
deeptools
updated 8 hours ago by
ATpoint
82k • written 12 hours ago by
Emily
▴ 20
0
votes
1
reply
99
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 7 hours ago by
ATpoint
82k • written 12 hours ago by
Pegasus
▴ 100
0
votes
2
replies
111
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
7 hours ago by
IdaHao0921
• 0
0
votes
4
replies
189
views
Galaxy StringTie error
stringtie
galaxy
5 hours ago by
trkfs
• 0
0
votes
3
replies
109
views
How to access GWAVA software of data
GWAVA
updated 3 hours ago by
GenoMax
142k • written 6 hours ago by
nonaddldy
▴ 10
0
votes
0
replies
26
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 2 hours ago by
GenoMax
142k • written 3 hours ago by
Bhavya
• 0
0
votes
3
replies
104
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 2 hours ago by
GenoMax
142k • written 16 hours ago by
RNAseqer
▴ 270
0
votes
0
replies
25
views
Is there a real ground truth for CNV data?
CNV
2 hours ago by
jennyp0706
• 0
0
votes
1
reply
49
views
sci-RNA-seq
sci-RNA-seq
clusters
combinatorial
single
1 hour ago by
kilcdincer
▴ 10
0
votes
2
replies
40
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA
RNAseq
updated 15 minutes ago by
ntsopoul
▴ 60 • written 1 hour ago by
doramora
▴ 10
0
votes
5
replies
148
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
10 minutes ago by
ntsopoul
▴ 60
0
votes
1
reply
109
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 9 hours ago by
ATpoint
82k • written 15 hours ago by
Chen
• 0
0
votes
0
replies
74
views
reference-free assembly error assessment tools
assembly
23 hours ago by
lagartija
▴ 160
0
votes
3
replies
336
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
20 hours ago by
mropri
▴ 150
0
votes
2
replies
386
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
20 hours ago by
David Langenberger
11k
0
votes
1
reply
104
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 18 hours ago by
Ram
43k • written 20 hours ago by
eking28
• 0
0
votes
1
reply
105
views
Splitting Seurat object by sample layers
seurat
updated 18 hours ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
0
votes
3
replies
149
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 18 hours ago by
Ram
43k • written 1 day ago by
yau
• 0
0
votes
6
replies
377
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 18 hours ago by
Ram
43k • written 3 days ago by
ajbarrett98
• 0
0
votes
0
replies
111
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 18 hours ago by
Ram
43k • written 15 days ago by
atharvakarkare14
▴ 30
0
votes
1
reply
140
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Cancer-Research
ATAC-seq
updated 18 hours ago by
Ram
43k • written 7 days ago by
David
• 0
0
votes
1
reply
227
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 18 hours ago by
Ram
43k • written 4 days ago by
Nikki
• 0
0
votes
1
reply
117
views
How to process Bulk WES data?
WES
WGS
updated 18 hours ago by
GenoMax
142k • written 19 hours ago by
wyuan37
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 17 hours ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
0
votes
1
reply
115
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 17 hours ago by
GenoMax
142k • written 19 hours ago by
cedric.blais
• 0
0
votes
1
reply
96
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
16 hours ago by
Arton
• 0
0
votes
4
replies
2.2k
views
MGLTools does not work in windows 11
Autodock
MGLTools
windows
windows11
updated 13 hours ago by
Ashfaq
• 0 • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
0
replies
68
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
12 hours ago by
Holly
• 0
0
votes
0
replies
176
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
12 hours ago by
Emily
▴ 20
0
votes
3
replies
282
views
Snakemake wrapper issue
fastqc
snakemake
updated 11 hours ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
52 results • Page
1 of 2
Recent Votes
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Help with IGV abbreviation
Split multiallelic SNPs to biallelic from vcf
Filtering multi-allelic sites in VCF files
How To Separate Snp Variants From Indel Variants In The Same Vcf File
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Comment: Expression analysis of LncRNA from RNA-seq data
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Recent Replies
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
Answer: RNAseq RNA content
by
ntsopoul
▴ 60
I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which …
Comment: RNAseq RNA content
by
ATpoint
82k
What is "row RNA"?
Comment: Overlapping Ranges within Granges object
by
ATpoint
82k
I would probably collapse overlapping regions with `reduce` to create the second GRanges. Can you add some representative data? Using dput?
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.
▴ 30
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…
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