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43 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
6
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
10 minutes ago by
sansan_96
▴ 90
0
votes
1
reply
24
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
updated 33 minutes ago by
Mensur Dlakic
★ 27k • written 1 hour ago by
MarcosCosta
• 0
0
votes
1
reply
60
views
Genome Visualization Tools
bacterial
genome
updated 1 hour ago by
Ram
43k • written 2 hours ago by
dlera.lozano
• 0
1
vote
3
replies
83
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 1 hour ago by
Ram
43k • written 2 hours ago by
Prawesh
• 0
0
votes
1
reply
80
views
Using ggplotly in R
ggplot
ggplotly
updated 2 hours ago by
jared.andrews07
★ 16k • written 3 hours ago by
jen
▴ 10
0
votes
1
reply
82
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 3 hours ago by
GenoMax
142k • written 4 hours ago by
bioinfo
▴ 150
0
votes
3
replies
164
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 4 hours ago by
noodle
▴ 580 • written 8 hours ago by
doramora
▴ 10
0
votes
1
reply
76
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 4 hours ago by
LauferVA
4.2k • written 6 hours ago by
graeme.thorn
▴ 100
0
votes
1
reply
75
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
updated 5 hours ago by
GenoMax
142k • written 6 hours ago by
melissa.joubert
• 0
0
votes
0
replies
52
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
6 hours ago by
ramiro.barrantes
• 0
4
votes
1
reply
149
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
8 hours ago by
J.
▴ 40
0
votes
0
replies
59
views
Is there a real ground truth for CNV data?
CNV
8 hours ago by
jennyp0706
• 0
0
votes
3
replies
160
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 8 hours ago by
GenoMax
142k • written 23 hours ago by
RNAseqer
▴ 270
1
vote
1
reply
93
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 4 hours ago by
Ram
43k • written 9 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
50
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 9 hours ago by
GenoMax
142k • written 9 hours ago by
Bhavya
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 11 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
0
votes
6
replies
268
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
6 hours ago by
ntsopoul
▴ 60
0
votes
3
replies
154
views
How to access GWAVA software of data
GWAVA
updated 10 hours ago by
GenoMax
142k • written 13 hours ago by
nonaddldy
▴ 10
0
votes
1
reply
125
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 15 hours ago by
ATpoint
82k • written 22 hours ago by
Chen
• 0
0
votes
1
reply
115
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 14 hours ago by
ATpoint
82k • written 19 hours ago by
Pegasus
▴ 100
0
votes
1
reply
96
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 1 hour ago by
Ram
43k • written 19 hours ago by
Emily
▴ 20
1
vote
1
reply
142
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 15 hours ago by
zx8754
11k • written 22 hours ago by
ohtang7
▴ 40
0
votes
0
replies
62
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
16 hours ago by
Spring
• 0
0
votes
2
replies
129
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
13 hours ago by
IdaHao0921
• 0
0
votes
3
replies
301
views
Snakemake wrapper issue
fastqc
snakemake
updated 17 hours ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
86
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
19 hours ago by
Holly
• 0
2
votes
5
replies
218
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 19 hours ago by
Philipp Bayer
8.5k • written 22 hours ago by
林明德
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 1 hour ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
1
reply
108
views
Filtering based on alternate allelic balance
GATK
VCF
updated 1 hour ago by
Ram
43k • written 23 hours ago by
Arton
• 0
2
votes
4
replies
171
views
Help with IGV abbreviation
igv
updated 1 hour ago by
Ram
43k • written 23 hours ago by
GeneC
• 0
0
votes
1
reply
129
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 23 hours ago by
GenoMax
142k • written 1 day ago by
cedric.blais
• 0
1
vote
5
replies
402
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 1 hour ago by
Ram
43k • written 6 days ago by
Prawesh
• 0
1
vote
2
replies
234
views
How to interpret infinite odds ratio?
statistics
12 hours ago by
Lukas
• 0
0
votes
4
replies
216
views
Galaxy StringTie error
stringtie
galaxy
12 hours ago by
trkfs
• 0
1
vote
3
replies
220
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
14 hours ago by
Vijith
▴ 30
3
votes
2
replies
250
views
imputation through beagle
panel
beagle
reference
imputation
15 hours ago by
analyst
▴ 50
2
votes
4
replies
277
views
BWA alignment
Samtools
bam
updated 15 hours ago by
ATpoint
82k • written 1 day ago by
Vahid
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 11 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
3
votes
3
replies
317
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 23 hours ago by
Mathew
▴ 140 • written 3 days ago by
Christopher
• 0
4
votes
7
replies
383
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
22 hours ago by
Chen
• 0
0
votes
0
replies
178
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
19 hours ago by
Emily
▴ 20
2
votes
3
replies
265
views
Finding variants within a subset of a BAM file
variant
calling
6 hours ago by
ramiro.barrantes
• 0
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 22 hours ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
43 results • Page
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Recent Votes
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
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?
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Recent Replies
Answer: Doubt about the process of annotation, detection, identification and classificat
by
Mensur Dlakic
★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Ram
43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
• 0
thanks, it's working now.
Comment: Genome Visualization Tools
by
GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Trivas
★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R
by
jared.andrews07
★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran
by
GenoMax
142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
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 …
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