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116,923 results • Page
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19
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RNAseq RNA content
mRNA
Linux
rRNA
RNA
RNAseq
updated 4 minutes ago by
ATpoint
82k • written 43 minutes ago by
doramora
▴ 10
1
vote
1
reply
91
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
59 minutes ago by
J.
▴ 10
0
votes
0
replies
21
views
Is there a real ground truth for CNV data?
CNV
1 hour ago by
jennyp0706
• 0
0
votes
3
replies
89
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 1 hour ago by
GenoMax
142k • written 15 hours ago by
RNAseqer
▴ 270
0
votes
1
reply
38
views
sci-RNA-seq
sci-RNA-seq
clusters
combinatorial
single
20 minutes ago by
kilcdincer
▴ 10
0
votes
0
replies
23
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 2 hours ago by
GenoMax
142k • written 2 hours ago by
Bhavya
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 4 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
0
votes
4
replies
137
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 34 minutes ago by
ATpoint
82k • written 14 hours ago by
ntsopoul
▴ 60
0
votes
3
replies
105
views
How to access GWAVA software of data
GWAVA
updated 2 hours ago by
GenoMax
142k • written 5 hours ago by
nonaddldy
▴ 10
0
votes
1
reply
106
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 8 hours ago by
ATpoint
82k • written 14 hours ago by
Chen
• 0
0
votes
1
reply
94
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 6 hours ago by
ATpoint
82k • written 11 hours ago by
Pegasus
▴ 100
795
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
77
views
What is the bin size for Bamcompare?
bin
chipseq
size
bamcompare
deeptools
updated 8 hours ago by
ATpoint
82k • written 11 hours ago by
Emily
▴ 20
1
vote
1
reply
116
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 7 hours ago by
zx8754
11k • written 15 hours ago by
ohtang7
▴ 40
0
votes
0
replies
49
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
9 hours ago by
Spring
• 0
0
votes
2
replies
109
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
6 hours ago by
IdaHao0921
• 0
0
votes
3
replies
279
views
Snakemake wrapper issue
fastqc
snakemake
updated 10 hours ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
65
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
11 hours ago by
Holly
• 0
2
votes
5
replies
193
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 11 hours ago by
Philipp Bayer
8.5k • written 15 hours ago by
林明德
• 0
0
votes
4
replies
2.2k
views
MGLTools does not work in windows 11
Autodock
MGLTools
windows
windows11
updated 12 hours ago by
Ashfaq
• 0 • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
1
reply
95
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
15 hours ago by
Arton
• 0
1
vote
4
replies
139
views
Help with IGV abbreviation
Genome
browser
14 hours ago by
GeneC
• 0
0
votes
1
reply
115
views
How to process Bulk WES data?
WES
WGS
updated 17 hours ago by
GenoMax
142k • written 18 hours ago by
wyuan37
• 0
0
votes
1
reply
114
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 16 hours ago by
GenoMax
142k • written 19 hours ago by
cedric.blais
• 0
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
19 hours ago by
David Langenberger
11k
0
votes
1
reply
103
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 17 hours ago by
Ram
43k • written 19 hours ago by
eking28
• 0
1
vote
4
replies
367
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 19 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
1
vote
3
replies
326
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
20 hours ago by
kalavattam
▴ 190
1
vote
2
replies
200
views
How to interpret infinite odds ratio?
statistics
5 hours ago by
Lukas
• 0
1
vote
2
replies
130
views
Duplicated sequence samtools
bowtie2
samtools
updated 21 hours ago by
GenoMax
142k • written 22 hours ago by
Moinuddin
• 0
0
votes
0
replies
73
views
reference-free assembly error assessment tools
assembly
22 hours ago by
lagartija
▴ 160
1
vote
2
replies
166
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 22 hours ago by
lagartija
▴ 160 • written 1 day ago by
Esraa
• 0
1
vote
0
replies
94
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
23 hours ago by
Biostar
2.8k
0
votes
1
reply
104
views
Splitting Seurat object by sample layers
seurat
updated 17 hours ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
0
votes
4
replies
187
views
Galaxy StringTie error
stringtie
galaxy
4 hours ago by
trkfs
• 0
0
votes
0
replies
73
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
1 day ago by
atariw
▴ 10
0
votes
1
reply
121
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 1 day ago by
GenoMax
142k • written 1 day ago by
octpus616
▴ 100
1
vote
3
replies
202
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
7 hours ago by
Vijith
▴ 30
0
votes
1
reply
125
views
consensus sequence calling
consensus
updated 23 hours ago by
bk11
★ 2.4k • written 1 day ago by
Ghada
• 0
0
votes
3
replies
148
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 17 hours ago by
Ram
43k • written 1 day ago by
yau
• 0
3
votes
2
replies
239
views
imputation through beagle
panel
beagle
reference
imputation
7 hours ago by
analyst
▴ 50
0
votes
0
replies
71
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
1 day ago by
JACKY
▴ 140
0
votes
1
reply
443
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 1 day ago by
aw7
▴ 280 • written 24 days ago by
abhishekghadge
• 0
1
vote
1
reply
189
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 1 day ago by
aw7
▴ 280 • written 5 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
86
views
Reference panel of normals for ensembl named refgenome
Mutect2
1 day ago by
gernophil
▴ 80
1
vote
0
replies
84
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
1 day ago by
tomas4482
▴ 400
2
votes
4
replies
266
views
BWA alignment
Samtools
bam
updated 8 hours ago by
ATpoint
82k • written 1 day ago by
Vahid
• 0
3
votes
2
replies
164
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 1 day ago by
ATpoint
82k • written 1 day ago by
jennyp0706
• 0
0
votes
1
reply
144
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 1 day ago by
Philipp Bayer
8.5k • written 1 day ago by
samRayne
• 0
0
votes
1
reply
227
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 17 hours ago by
Ram
43k • written 4 days ago by
Nikki
• 0
116,923 results • Page
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Error: htsjdk.tribble.TribbleExpection: The provided VCF file is malformed at approximately line number 5880: Duplicate allele added to VariantContext: GT
Answer: Process Truncated fastq file
The Biostar Herald for Monday, May 13, 2024
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A: What % of rRNA contamination is acceptable?
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Comment: Help with IGV abbreviation
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Recent Replies
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.
▴ 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 …
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