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26 results • Page
1 of 1
Sort: replies
Rank
Views
Votes
Replies
0
votes
10
replies
1.4k
views
How to translate CDS to an amino acid sequence
translation
CDS
sequencing
updated 18 hours ago by
vvasta
• 0 • written 8 months ago by
Max
• 0
2
votes
7
replies
273
views
How to Calulate Allele Frequency from a VCF File?
frequency
allele
VCF
7 minutes ago by
Emoji
• 0
8
votes
6
replies
343
views
Gene Set Enrichment Analysis, pathway, metabolism
metabolism
pathway
GSEA
17 hours ago by
Rob
▴ 160
3
votes
4
replies
311
views
Is there a command to annotate genes from a txt file?
scRNA
python
22 minutes ago by
mt_pereira
• 0
2
votes
4
replies
237
views
How to continue a interrupted MrBayes tree analysis?
MrBayes
updated 1 hour ago by
omaridris5315
• 0 • written 5 days ago by
超
• 0
0
votes
2
replies
1.3k
views
MrBayes tree in RAxML
RAxML
updated 1 hour ago by
omaridris5315
• 0 • written 4.8 years ago by
F.I.2011
▴ 10
0
votes
2
replies
175
views
How possible deadlocks are there while migrating from MYISAM to InnoDb?
dbms
updated 18 hours ago by
Pierre Lindenbaum
152k • written 22 hours ago by
jessewhite8077
• 0
1
vote
2
replies
241
views
Recommendations needed for a tool for comparative gene set enrichment analyses via a webserver
set
webserver
enrichment
gene
analyses
3 hours ago by
fuellen
▴ 20
0
votes
2
replies
2.0k
views
trainGlimmerHMM Error while training a genome
software error
updated 10 hours ago by
congliu37
• 0 • written 6.7 years ago by
swati.6783
▴ 10
1
vote
2
replies
103
views
a problem with getBM
and
getBM
biomart
3 hours ago by
sanaz
• 0
0
votes
1
reply
86
views
how to do a reliable single cell sequencing analysis?
singlecell
updated 3 hours ago by
ATpoint
68k • written 8 hours ago by
apple4lee
• 0
0
votes
1
reply
171
views
Error 134 while aligning using hisat2
hisat2
alignment
sam
bam
updated 22 hours ago by
Fabio Marroni
★ 2.9k • written 5 days ago by
Ngrin
• 0
0
votes
1
reply
174
views
Statistical test for checking cis regulation?
Genomics
Biostats
updated 22 hours ago by
Fabio Marroni
★ 2.9k • written 5 days ago by
lumos
• 0
0
votes
1
reply
132
views
translate CDS to prot formatted with nt nubers
tool
translate
updated 17 hours ago by
Pierre Lindenbaum
152k • written 18 hours ago by
vvasta
• 0
1
vote
1
reply
166
views
How to calculate tumor mutation burden (TMB)?
TMB
Mutations
WES
Sequencing
Mutationrate
updated 17 hours ago by
Fabio Marroni
★ 2.9k • written 18 days ago by
tanbiswas6
▴ 10
0
votes
1
reply
244
views
**Error: unable to open file or unable to determine types for file**
bedtools
updated 23 hours ago by
Pierre Lindenbaum
152k • written 1 day ago by
Neel
▴ 10
1
vote
1
reply
49
views
How to calculate Minion run time needed?
Minion
updated 1 hour ago by
andres.firrincieli
3.1k • written 2 hours ago by
ve9
▴ 50
0
votes
1
reply
59
views
mrbayes checkpoint file not starting from linux or windows after accidental closing
mrbayes
1 hour ago by
omaridris5315
• 0
0
votes
1
reply
122
views
transcriptomincs
assembly
transcriptome
updated 18 minutes ago by
Apex92
▴ 240 • written 1 day ago by
Kiran
• 0
0
votes
0
replies
40
views
getTable ignores query ranges
rtracklayer
2 hours ago by
Kyle
• 0
0
votes
0
replies
84
views
maximum fastq file size in galaxy?
fastq
rna-seq
usegalaxy
15 hours ago by
demoraesdiogo2017
▴ 80
0
votes
0
replies
130
views
Functional annotation results with Eggnog mapper, For a same query several COGs, several GO:....
COGs
GOs
results
Eggnog
22 hours ago by
F.Bedjou
• 0
0
votes
0
replies
10
views
Normalizing expression values
bioinformatics
logCPM
normalization
Scanpy
scRNA
24 minutes ago by
mt_pereira
• 0
0
votes
0
replies
57
views
Machine Learning Classifiers on TCGA dataset(tpm_unstrand) gene expression data set
machine
RNASeq
python
learning
2 hours ago by
Jakpa
▴ 50
0
votes
0
replies
132
views
How quality score for somatic mutations in ICGC was calculated
somatic
mutations
ICGC
22 hours ago by
caochch
• 0
0
votes
0
replies
7
views
Scanpy - highest expressed genes
bioinformatics
expressed
normalization
highest
Scanpy
scRNA
genes
13 minutes ago by
mt_pereira
• 0
26 results • Page
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Recent Votes
Comment: How to Calulate Allele Frequency from a VCF File?
Answer: Is there a command to annotate genes from a txt file?
Answer: Single cell RNA-seq analysis
A: LogFC and LogCPM
A: BWA shm index preloading: only for BWA MEM?
Comment: How to calculate Minion run time needed?
A: question about MrBayes software: evolutionary models
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Recent Replies
Comment: How to Calulate Allele Frequency from a VCF File?
by
Emoji
• 0
Thanks, but how do i do that?
Answer: transcriptomincs
by
Apex92
▴ 240
Yes, you can use a reference genome from a related species to assemble transcripts of a target species. This approach is known as ```de nov…
Answer: MrBayes tree in RAxML
by
omaridris5315
• 0
any tree is a valid hypothesis
Answer: How to continue a interrupted MrBayes tree analysis?
by
omaridris5315
• 0
Hello Mensur, Could you look at my case too? interruption issue but a different error. This is the second time I face and I rerun it. I ha…
Answer: mrbayes checkpoint file not starting from linux or windows after accidental clos
by
omaridris5315
• 0
my convergence value at 23 million run for last 10 days was at .017623 something. out of 7 million more remaining.
Comment: How to calculate Minion run time needed?
by
andres.firrincieli
3.1k
> Does someone know how to calculate how many hours (approximately) i > need to run an minion, to get a good coverage for example of bacter…
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…
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