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137 results • Page
3 of 3
Sort: Rank
Rank
Views
Votes
Replies
3
votes
6
replies
520
views
SV calling using giraffe/vg
vg
Giraffe
calling
structural
variant
6 days ago by
TN
• 0
1
vote
1
reply
160
views
How to calculate tumor mutation burden (TMB)?
TMB
Mutations
WES
Sequencing
Mutationrate
updated 14 hours ago by
Fabio Marroni
★ 2.9k • written 18 days ago by
tanbiswas6
▴ 10
0
votes
1
reply
216
views
FRiP value
FRiP
updated 2 days ago by
ATpoint
68k • written 19 days ago by
michelafrancesconi9
• 0
4
votes
4
replies
699
views
Analysis of Nanopore cDNA sequencing data
alignment
nanopore
sequencing
minimap2
2 days ago by
Nico80
▴ 60
0
votes
1
reply
299
views
Eggnog mapper -> Blast2Go for Gene Ontology??
blast2go
eggnog
mapper
GO
updated 5 days ago by
F.Bedjou
• 0 • written 5 months ago by
Megan
• 0
0
votes
1
reply
252
views
homer not configured properly
Homer
makeTagDirectory
updated 4 days ago by
meg_c3
• 0 • written 8 months ago by
amahdi779
• 0
1
vote
1
reply
447
views
Downloading the IMGT/V-QUEST software
vquest
software
updated 4 days ago by
H.Hasani
▴ 990 • written 14 months ago by
rubic
▴ 260
0
votes
3
replies
581
views
CDSeq for deconvolution of whole blood RNAseq, any experience?
RNAseq
Deconvolution
updated 3 days ago by
FrankStarling
▴ 20 • written 15 months ago by
Barista
▴ 20
0
votes
1
reply
1.3k
views
Haploview Aggressive Tagging no output
Haploview
tagging
output
updated 2 days ago by
Famf
▴ 20 • written 6.0 years ago by
sidwell
▴ 10
0
votes
2
replies
1.1k
views
Where to download Hedenfalk gene data?
genome
R
updated 4 days ago by
Ram
37k • written 6.4 years ago by
selmerca
• 0
0
votes
1
reply
2.7k
views
Haploview command line: get TagSNP
Haploview
TagSNP
Haplotype
updated 2 days ago by
Famf
▴ 20 • written 6.5 years ago by
nsounac
• 0
0
votes
0
replies
3.0k
views
Targetscan context+ score
miR-targets
TargetScan
updated 5 days ago by
Ram
37k • written 7.7 years ago by
navesjuan
• 0
1
vote
0
replies
2.3k
views
Scoring matrix of 3 sequence alignment
sequencing
multiple-sequencing
updated 4 days ago by
Ram
37k • written 7.7 years ago by
mhasa006
▴ 70
0
votes
1
reply
2.1k
views
Extracting FASTA Sequence by Transcriptomic Coordinates
fasta
star
transcriptome
updated 4 days ago by
Ram
37k • written 7.7 years ago by
eyal.peer
• 0
4
votes
10
replies
3.5k
views
TCGA normalized count data of 1000 samples for DGE
RNA-Seq
TCGA
updated 4 days ago by
Ram
37k • written 7.7 years ago by
David_emir
▴ 460
1
vote
5
replies
2.5k
views
who can give me the data of genome music bmr calc-covg
genome
music
bmr
calc-covg
updated 4 days ago by
Ram
37k • written 7.7 years ago by
qwertyuiop201320142015
• 0
0
votes
4
replies
2.6k
views
biomaRt: Extracting data for a particular isoform (R/bioconductor)
bioconductor
utr
biomart
updated 4 days ago by
Ram
37k • written 7.7 years ago by
bsmith030465
▴ 210
0
votes
0
replies
2.9k
views
Maximum likelihood user tree analysis in MEGA !
Mega
genetic-distance
updated 5 days ago by
Ram
37k • written 7.7 years ago by
morteza.mahmoudisaber
▴ 80
0
votes
0
replies
1.8k
views
How efficiently to use information of two de novo assembled transcriptome for further analysis?
Assembly
RNA-Seq
next-gen-sequencing
updated 4 days ago by
Ram
37k • written 7.7 years ago by
seta
★ 1.7k
0
votes
1
reply
1.2k
views
find NON Coding SNPs using annovar or ucsc genome browser
ucsc
SNP
orf
non-coding
annovar
updated 5 days ago by
Ram
37k • written 7.7 years ago by
pinikoma
• 0
0
votes
0
replies
1.3k
views
How do you download annotations from gramene database
next-gen
snp
gene
sequence
updated 5 days ago by
Ram
37k • written 7.7 years ago by
p.weru
• 0
0
votes
0
replies
1.2k
views
Information to obtain collaboration or resources for HTS
RNA-Seq
next-gen-sequencing
updated 5 days ago by
Ram
37k • written 7.7 years ago by
mgadrianam
▴ 30
0
votes
0
replies
1.5k
views
Cluster distance for nextseq, miseq and hiseq 2500 (for picard's markduplicates)
hiseq
miseq
duplicates
picard
nextseq
updated 5 days ago by
Ram
37k • written 7.7 years ago by
Brad Langhorst
▴ 120
3
votes
5
replies
6.2k
views
Converting Vcftools output to R readable format
vcf
SNP
R
vcftools
updated 5 days ago by
Ram
37k • written 7.7 years ago by
pifferdavide
▴ 100
2
votes
3
replies
10k
views
converting maf to vcf
Exome
maf2vcf
updated 5 days ago by
Ram
37k • written 7.7 years ago by
ashishchahl
• 0
0
votes
0
replies
1.8k
views
How to calculate base pair conservation for two species?
conservation-score
updated 4 days ago by
Ram
37k • written 7.7 years ago by
notsway
• 0
0
votes
2
replies
2.1k
views
Biopython ; pdb file parsing
PDB
biopython
updated 4 days ago by
Ram
37k • written 7.7 years ago by
fareehakanwal90
▴ 30
0
votes
0
replies
1.1k
views
Hotspot error during run_pass2_hotspot and during run_10kb_counts
software-error
updated 4 days ago by
Ram
37k • written 7.7 years ago by
scambier
• 0
0
votes
0
replies
1.5k
views
Software to perform GxE iGWAS for a binary disease with a quantitative E factor.
iGWAS
updated 4 days ago by
Ram
37k • written 7.7 years ago by
aleix.arnau1990
▴ 10
4
votes
8
replies
1.9k
views
Select only sequences that align with X% of a query during blastp search
sequence
blast
alignment
updated 4 days ago by
Ram
37k • written 7.7 years ago by
dago
★ 2.7k
2
votes
1
reply
1.2k
views
pair wise differences of different populations
snp
updated 4 days ago by
Ram
37k • written 7.7 years ago by
drshahzadbhatti
• 0
0
votes
0
replies
1.1k
views
Repeatedly running Tagger provides different results
SNP
updated 4 days ago by
Ram
37k • written 7.7 years ago by
biobio
• 0
4
votes
2
replies
2.3k
views
Signal Distribution Charts
ChIP-Seq
next-gen
R
updated 4 days ago by
Ram
37k • written 7.7 years ago by
John
13k
0
votes
2
replies
2.1k
views
Get bedgraph file from CEL affymetrix file
chip
cel
transcriptome
updated 4 days ago by
Ram
37k • written 7.7 years ago by
flyamer
▴ 60
0
votes
3
replies
1.8k
views
consistency in sequence alignment?
alignment
sequence
updated 4 days ago by
Ram
37k • written 7.7 years ago by
lait
▴ 170
0
votes
0
replies
819
views
Is any body here familiar with COMODO v1.0: (COnserved MODules across Organims)?
COMODO
updated 4 days ago by
Ram
37k • written 7.7 years ago by
nazaninhoseinkhan
▴ 490
0
votes
2
replies
2.5k
views
convert transdecoder gff3 in to simple gff structure for genemarkET
GenemarkET
transdecoder
rna-seq
updated 4 days ago by
Ram
37k • written 7.7 years ago by
amoltej
▴ 90
137 results • Page
3 of 3
Recent Votes
A: Using ColSums vs sizeFactors in read count normalization
Comment: a problem with getBM
C: Reorder heatmap rows in a dataset with missing values
A: Difference between GTF file with CHR and without CHR. ENSEMBL
Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
Comment: bgzip error 4
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Teacher
to
ATpoint
68k
Popular Question
to
tianshenbio
▴ 160
Popular Question
to
maxdlf12
• 0
Teacher
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Pierre Lindenbaum
152k
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LDT
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Michael Dondrup
52k
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caochch
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Recent Replies
Answer: how to do a reliable single cell sequencing analysis?
by
ATpoint
68k
The usual approach for starters would be to follow guided and well-accepted tutorials. That would (incomplete list) be: - The Biocon…
Answer: a problem with getBM
by
sanaz
• 0
head(ensembl_ids) X baseMean log2FoldChange lfcSE stat pvalue padj 1 ENSG00000000938.13 1344.2587 2.107…
Answer: Recommendations needed for a tool for comparative gene set enrichment analyses v
by
fuellen
▴ 20
Hello and Thanks! OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared". In any case, is …
Comment: a problem with getBM
by
Mike Smith
★ 1.9k
Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`. It's …
Answer: trainGlimmerHMM Error while training a genome
by
congliu37
• 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File?
by
Jeremy Leipzig
21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)?
by
Fabio Marroni
★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism
by
Rob
▴ 160
Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers
by
Pierre Lindenbaum
152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence
by
vvasta
• 0
I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
by
Pierre Lindenbaum
152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
by
Pierre Lindenbaum
152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation?
by
Fabio Marroni
★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2
by
Fabio Marroni
★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file**
by
Pierre Lindenbaum
152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
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