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Showing top results for tag:
ploidy
•
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0
votes
0
replies
206
views
whatshap ploidy error on female sample
ONT
ploidy
phasing
nanopore
updated 6 weeks ago by
Ram
44k • written 6 weeks ago by
eebloom
▴ 80
1
vote
1
reply
352
views
Genome Analysis Insights: BUSCO Evaluation of Repetitive Elements and Ploidy Level in Crocus sativus"
coverage
ploidy
complex-genome
BUSCO
updated 8 months ago by
Ram
44k • written 8 months ago by
mathavanbioinfo
▴ 80
0
votes
2
replies
787
views
Does ploidy in variant calling affect admixture detection with TreeMix?
ploidy
admixture
SNP
TreeMix
11 months ago by
Michael
55k
0
votes
0
replies
335
views
ChIPseq w/ polyploid genome : Xenopus laevis
chipseq
alignment
xenopus
ploidy
18 months ago by
William
▴ 10
0
votes
0
replies
498
views
Protocol to detect chromosomal ploidy from WGS VCF?
wgs
ploidy
20 months ago by
optimistsso4co3
▴ 110
2
votes
0
replies
441
views
Absolute and relative Copy numbers, tumor and ploidy
number
copy
ploidy
tumor
22 months ago by
ashenflower
▴ 30
1
vote
1
reply
950
views
Convert haploid chrX to homozygous diploid in VCF
vcf
beagle
ploidy
updated 2.1 years ago by
Pierre Lindenbaum
164k • written 2.1 years ago by
ThunderPhoenix
• 0
0
votes
1
reply
542
views
Get information from Kew database in batch
DNA
C-values
ploidy
database
Kew
updated 2.4 years ago by
colindaven
6.7k • written 2.4 years ago by
triplee0305
▴ 10
2
votes
4
replies
726
views
Searching for tool to assign data as haploid or diploid
Ploidy
WGS
2.5 years ago by
Naomi
• 0
0
votes
2
replies
842
views
Ploidy in WGS samples
cancer
WGS
NGS
bam
ploidy
updated 2.6 years ago by
Thind amarinder
▴ 340 • written 2.7 years ago by
loy_loy
▴ 10
2
votes
0
replies
608
views
GT field in a 8 ploidy vcf
Freebayes
GT
ploidy
vcf
2.9 years ago by
Michal Nevo
▴ 140
0
votes
2
replies
2.3k
views
freebayes for snp call in pooled samples: how do I set the parameters?
SNP
freebayes
pooled
ploidy
updated 3.5 years ago by
ross_whetten
▴ 10 • written 4.5 years ago by
cristiana.ij.marques
• 0
1
vote
0
replies
626
views
Estimate ploidy and purity in cancer targeted sequencing
ploidy
purity
targeted sequencing
3.6 years ago by
rosefroehlich
▴ 10
0
votes
3
replies
4.4k
views
WES samples failing ABSOLUTE
absolute
WES
ploidy
purity
updated 3.7 years ago by
jingnany0
• 0 • written 7.1 years ago by
mkaushal
▴ 120
2
votes
1
reply
2.0k
views
How can you determine ploidy of a genome?
ploidy
kmer
genomescope
jellyfish
updated 4.1 years ago by
h.mon
35k • written 4.1 years ago by
kristina.mahan
▴ 170
0
votes
1
reply
1.0k
views
BBnorm not outputting txt files when trying to determine ploidy on pb fastq.gz reads
kmer
khist
bbnorm
bbmap
ploidy
updated 4.2 years ago by
GenoMax
145k • written 4.2 years ago by
kristina.mahan
▴ 170
0
votes
0
replies
1.0k
views
Change ploidy level of SNP genotypes vcf in r
SNP
R
VCF
PLOIDY
4.3 years ago by
irieljoerin
▴ 40
0
votes
0
replies
574
views
Ploidy of genome assembled from PacBio reads
genome
next-gen
PacBio
ploidy
4.9 years ago by
ambarishnag
• 0
0
votes
1
reply
3.0k
views
Determining ploidy via read ratios with HaplotypeCaller: skewed results?
SNP
gatk
ploidy
illumina
R
updated 5.1 years ago by
Biostar
20 • written 7.9 years ago by
mmats010
▴ 80
10
votes
17
replies
4.1k
views
Ploidy Correction In NGS cancer data (human)
CNV
ploidy
cancer
5.3 years ago by
German.M.Demidov
★ 2.9k
2
votes
1
reply
2.7k
views
ABSOLUTE output interpretation
ABSOLUTE
purity
ploidy
SCNA
updated 5.4 years ago by
Kevin Blighe
88k • written 5.4 years ago by
9521ljh
▴ 50
0
votes
0
replies
931
views
Tools to access variation of ploidy at certain genomic loci using WES
WES
Ploidy
Endomitosis
5.4 years ago by
Rahul Sharma
▴ 660
2
votes
6
replies
2.1k
views
VCFParseError: ploidy > 2 not supported
VCF
GATK
PLOIDY
updated 5.6 years ago by
tpoterba
▴ 50 • written 5.8 years ago by
always_learning
★ 1.1k
0
votes
1
reply
1.5k
views
readSnpMatrix in FACETS gives error
CNV
Purity
Ploidy
FACETS
6.4 years ago by
hsbinf
▴ 30
1
vote
6
replies
2.2k
views
Ploidy Analysis in R
R
SNP
Methylation
450K
ploidy
updated 6.6 years ago by
Kevin Blighe
88k • written 6.6 years ago by
gargar
• 0
0
votes
0
replies
1.6k
views
Parameters for ABSOLUTE on WGS data
next-gen
ABSOLUTE
tumor purity
ploidy
7.3 years ago by
shiyang93
▴ 70
0
votes
0
replies
1.3k
views
Is there any literature for using kmer counting to determine ploidy?
ploidy
NGS
7.4 years ago by
tayte_campbell
• 0
2
votes
0
replies
1.9k
views
What is Cancer or tumor purities and ploidies
Purity
Ploidy
7.5 years ago by
akij
▴ 190
5
votes
8
replies
5.7k
views
estimating tumor purity and ploidy and CNV
purity
ploidy
CNV
updated 7.6 years ago by
Eric T.
★ 2.8k • written 7.6 years ago by
Bogdan
★ 1.4k
2
votes
6
replies
6.8k
views
How to "haploidize" diploid SNPs data in a vcf file
vcf
SNP
ploidy
updated 7.6 years ago by
Len Trigg
★ 1.6k • written 7.6 years ago by
BioinfoNovice
▴ 110
2
votes
10
replies
3.4k
views
Determine ploidy using SNP-Calling
SNP
mapping
ploidy
NGS
7.6 years ago by
dilution
• 0
2
votes
1
reply
4.7k
views
Ploidy vs. copy number in Sequenza
sequenza
depth ratio
copy number
ploidy
updated 7.9 years ago by
favero.francesco
▴ 120 • written 7.9 years ago by
wclee47
• 0
2
votes
2
replies
3.8k
views
Database for plant ploidy
ploidy
database
public
updated 8.9 years ago by
Renesh
★ 2.2k • written 8.9 years ago by
Anand Rao
▴ 640
0
votes
1
reply
2.1k
views
ABSOLUTE tends to give high ploidy result
geonome
purity
ploidy
ABSOLUTE
9.1 years ago by
wangjq
▴ 10
2
votes
2
replies
3.0k
views
Are there any software packages available to calculate ploidy from RNA-Seq data?
RNA-Seq
CNV
ploidy
updated 23 months ago by
Ram
44k • written 9.2 years ago by
JacobS
▴ 990
35 results • Page
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Comment: Sankey + dot plot
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zx8754
12k
What is the problem, where is the code you are trying? Provide code, example data, expected output.
Answer: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
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55k
Something went wrong during star alignments of samples OE1_2, OE1_3, and OE_NC_1. The obvious place to look for the reason is in the Star l…
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164k
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Comment: How to compile Multiz
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Santex
• 0
I'm sorry. I post a new question.
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I solved the problem by installing `NMF` package.
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
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145k
Can you check using `featureCounts` to make sure things look reasonable with alignments? You could also use `salmon` to do transcript quant…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
Since we don't have access to your data we can't comment. Check the integrity of your input data files. Validate the files if you are not s…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
https://www.biostars.org/u/145859/ : Use `ADD REPLY/ADD COMMENT` to add additional information to existing threads. `ADD YOUR ANSWER` is me…
Comment: How to compile Multiz
by
GenoMax
145k
Please do not ask questions unrelated to the original post in this thread. Post a new question.
Comment: How to compile Multiz
by
Santex
• 0
I could install multiz from it! Thank you very much. Please help me out with the problem below. I run multiz like below. (myenv) tak…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
One of them looks okay, but I don't quite believe it. ```R > table(df$`intermediate_data.OE1_1_.genes.results`==0) FALSE TRUE 21200 2…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
It seems that the files that generated the results also have significant issues. Except for one sample, all other samples only have over 20…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
Their .fq files all look similar, should I rerun these programs?
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
> Cannot open intermediate_data/OE_NC_2_.temp/OE_NC_2__alignable_1.fq! It may not exist. Looks like you are missing some files. BTW this …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
The most torturous thing is that some groups did indeed generate results. ``` ls intermediate_data KO1_1_.stat KO1_3_.isoforms…
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