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52 results • Page
1 of 2
Sort: Votes
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Views
Votes
Replies
4
votes
7
replies
380
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
18 hours ago by
Chen
• 0
4
votes
1
reply
126
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
4 hours ago by
J.
▴ 40
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 7 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
3
votes
2
replies
243
views
imputation through beagle
panel
beagle
reference
imputation
11 hours ago by
analyst
▴ 50
3
votes
3
replies
315
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 19 hours ago by
Mathew
▴ 140 • written 3 days ago by
Christopher
• 0
3
votes
3
replies
254
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 20 hours ago by
Ram
43k • written 14 days ago by
Adyasha
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 7 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
2
votes
4
replies
149
views
Help with IGV abbreviation
Genome
browser
18 hours ago by
GeneC
• 0
2
votes
4
replies
274
views
BWA alignment
Samtools
bam
updated 11 hours ago by
ATpoint
82k • written 1 day ago by
Vahid
• 0
2
votes
3
replies
251
views
Finding variants within a subset of a BAM file
variant
calling
2 hours ago by
ramiro.barrantes
• 0
2
votes
5
replies
201
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 15 hours ago by
Philipp Bayer
8.5k • written 18 hours ago by
林明德
• 0
1
vote
3
replies
332
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
23 hours ago by
kalavattam
▴ 190
1
vote
4
replies
371
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 22 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
1
vote
2
replies
217
views
How to interpret infinite odds ratio?
statistics
8 hours ago by
Lukas
• 0
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 18 hours ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
1
vote
1
reply
125
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 11 hours ago by
zx8754
11k • written 18 hours ago by
ohtang7
▴ 40
1
vote
1
reply
68
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 36 minutes ago by
Ram
43k • written 5 hours ago by
kilcdincer
▴ 10
1
vote
3
replies
208
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
10 hours ago by
Vijith
▴ 30
1
vote
4
replies
324
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 21 hours ago by
Ram
43k • written 5 days ago by
samRayne
• 0
0
votes
1
reply
85
views
What is the bin size for Bamcompare?
bin
chipseq
size
bamcompare
deeptools
updated 11 hours ago by
ATpoint
82k • written 15 hours ago by
Emily
▴ 20
0
votes
1
reply
114
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 11 hours ago by
ATpoint
82k • written 18 hours ago by
Chen
• 0
0
votes
1
reply
104
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 10 hours ago by
ATpoint
82k • written 15 hours ago by
Pegasus
▴ 100
0
votes
2
replies
116
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
9 hours ago by
IdaHao0921
• 0
0
votes
4
replies
200
views
Galaxy StringTie error
stringtie
galaxy
8 hours ago by
trkfs
• 0
0
votes
3
replies
130
views
How to access GWAVA software of data
GWAVA
updated 6 hours ago by
GenoMax
142k • written 9 hours ago by
nonaddldy
▴ 10
0
votes
0
replies
34
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 5 hours ago by
GenoMax
142k • written 5 hours ago by
Bhavya
• 0
0
votes
3
replies
137
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 4 hours ago by
GenoMax
142k • written 19 hours ago by
RNAseqer
▴ 270
0
votes
0
replies
37
views
Is there a real ground truth for CNV data?
CNV
4 hours ago by
jennyp0706
• 0
0
votes
6
replies
216
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
2 hours ago by
ntsopoul
▴ 60
0
votes
0
replies
26
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
2 hours ago by
ramiro.barrantes
• 0
0
votes
1
reply
40
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
updated 1 hour ago by
GenoMax
142k • written 2 hours ago by
melissa.joubert
• 0
0
votes
1
reply
32
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 50 minutes ago by
LauferVA
4.2k • written 2 hours ago by
graeme.thorn
▴ 100
0
votes
3
replies
98
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 19 minutes ago by
noodle
▴ 580 • written 4 hours ago by
doramora
▴ 10
0
votes
0
replies
7
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
13 minutes ago by
bioinfo
▴ 150
0
votes
3
replies
337
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
23 hours ago by
mropri
▴ 150
0
votes
2
replies
389
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
22 hours ago by
David Langenberger
11k
0
votes
1
reply
108
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 21 hours ago by
Ram
43k • written 23 hours ago by
eking28
• 0
0
votes
1
reply
108
views
Splitting Seurat object by sample layers
seurat
updated 21 hours ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
0
votes
3
replies
154
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 21 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 21 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 20 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 20 hours ago by
Ram
43k • written 7 days ago by
David
• 0
0
votes
1
reply
228
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 20 hours ago by
Ram
43k • written 4 days ago by
Nikki
• 0
0
votes
1
reply
120
views
How to process Bulk WES data?
WES
WGS
updated 20 hours ago by
GenoMax
142k • written 21 hours ago by
wyuan37
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 20 hours ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
0
votes
1
reply
120
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 19 hours ago by
GenoMax
142k • written 22 hours ago by
cedric.blais
• 0
0
votes
1
reply
99
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
18 hours ago by
Arton
• 0
0
votes
4
replies
2.2k
views
MGLTools does not work in windows 11
Autodock
MGLTools
windows
windows11
updated 15 hours ago by
Ashfaq
• 0 • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
0
replies
77
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
15 hours ago by
Holly
• 0
0
votes
0
replies
177
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
15 hours ago by
Emily
▴ 20
52 results • Page
1 of 2
Recent Votes
A: Best de novo assembler for insect genome ?
Comment: sci-RNA-seq
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Help with IGV abbreviation
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Recent Replies
Answer: RNAseq RNA content
by
noodle
▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file?
by
wyuan37
• 0
Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file?
by
wyuan37
• 0
Thanks! Super helpful.
Answer: Post-imputation QC for input into GWAS analyses
by
LauferVA
4.2k
1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data
by
GenoMax
142k
You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file
by
ramiro.barrantes
• 0
Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
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.
▴ 40
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 …
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