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30 results • Page
1 of 1
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Votes
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0
votes
0
replies
12
views
imputation through beagle
panel
beagle
reference
imputation
50 minutes ago by
analyst
▴ 50
0
votes
0
replies
12
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
1 hour ago by
analyst
▴ 50
0
votes
0
replies
27
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
3 hours ago by
melissachua90
▴ 70
0
votes
0
replies
51
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
8 hours ago by
Christopher
• 0
0
votes
1
reply
84
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
updated 10 hours ago by
Pierre Lindenbaum
161k • written 11 hours ago by
ajbarrett98
• 0
0
votes
10
replies
298
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
updated 11 hours ago by
swbarnes2
14k • written 18 hours ago by
Tuck898
• 0
1
vote
3
replies
124
views
Tassel 5 GBS: Is there something wrong with my fastqs?
tassel
fastq
gbs
updated 11 hours ago by
GenoMax
142k • written 13 hours ago by
meck
• 0
3
votes
3
replies
128
views
what is another word for a BLAST "hit"?
blast
alignment
13 hours ago by
dec986
▴ 380
1
vote
2
replies
98
views
Genome Assembly task + Protein Translation, assignment advice on a question
sequence-analysis
protein-synthesis
29 minutes ago by
rackbersingh
• 0
0
votes
1
reply
102
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 13 hours ago by
Ram
43k • written 15 hours ago by
Shwetha
• 0
0
votes
0
replies
65
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
16 hours ago by
beantkapoor16
• 0
0
votes
0
replies
68
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 13 hours ago by
Ram
43k • written 19 hours ago by
naomiboldon
• 0
1
vote
3
replies
164
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 13 hours ago by
Ram
43k • written 20 hours ago by
Omics data mining
▴ 260
1
vote
7
replies
480
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 22 hours ago by
Pierre Lindenbaum
161k • written 3 days ago by
schmince
• 0
0
votes
5
replies
189
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
18 hours ago by
SilhouetteQ
• 0
0
votes
1
reply
93
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 23 hours ago by
GenoMax
142k • written 23 hours ago by
maria.soler
• 0
0
votes
2
replies
131
views
How are score_weights calculated in this code?
single-cell
1 hour ago by
carolofharvest
▴ 40
0
votes
1
reply
128
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 15 hours ago by
curious
▴ 750 • written 1 day ago by
SeoGyun
• 0
3
votes
1
reply
116
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 22 hours ago by
dthorbur
★ 1.9k • written 1 day ago by
Eren
• 0
0
votes
2
replies
165
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 13 hours ago by
Ram
43k • written 1 day ago by
sainavyav22
• 0
3
votes
4
replies
240
views
Truncated metadata file report from ENA Portal API
ena
python
15 hours ago by
Giulia
• 0
1
vote
4
replies
279
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
13 hours ago by
rackbersingh
• 0
3
votes
5
replies
331
views
RNA seq analysis
DESeq
RNA-seq
22 hours ago by
prifa
▴ 10
1
vote
9
replies
339
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 21 hours ago by
i.sudbery
19k • written 3 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
4
replies
224
views
Correlation Analysis
statistics
methylation
NGS
expression
2 hours ago by
Researcher
▴ 30
0
votes
2
replies
251
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 15 hours ago by
GenoMax
142k • written 7 days ago by
Ximena
• 0
0
votes
0
replies
110
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
updated 11 hours ago by
GenoMax
142k • written 9 days ago by
meck
• 0
1
vote
4
replies
383
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 15 hours ago by
GenoMax
142k • written 23 days ago by
aniigodwinn
• 0
1
vote
4
replies
474
views
cellranger error message
multiplexing
cellranger
updated 19 hours ago by
Max
• 0 • written 12 weeks ago by
Alivia
▴ 10
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 17 hours ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
30 results • Page
1 of 1
Recent Votes
Comment: Genome Assembly task + Protein Translation, assignment advice on a question
Answer: Tissue-specific DEG analysis with DEseq2
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
Answer: what is another word for a BLAST "hit"?
Comment: what is another word for a BLAST "hit"?
Comment: what is another word for a BLAST "hit"?
Comment: How can I merge GFF files together to produce a file with gene functions from bo
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Popular Question
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melissachua90
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▴ 100
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10k
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Recent Replies
Comment: Genome Assembly task + Protein Translation, assignment advice on a question
by
rackbersingh
• 0
It is an indeed an old assignment question, I am doing revision and practicing answering questions for an upcoming test and just wanted to …
Comment: How are score_weights calculated in this code?
by
carolofharvest
▴ 40
I've found this code [in this site :][1] . It doesn't seem like they've shared any additional information about this in the previous line…
Comment: Correlation Analysis
by
Researcher
▴ 30
Thank you so much. I ran based on the above code and found that all gene columns have the same values, which you obtain as the average corr…
Answer: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
use bcftools merge with --force-samples and then use jvarkit https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ to replace the no-call …
Answer: In IGV is this a heterogeneous mutation or false call?
by
swbarnes2
14k
Since all the reads that show the alternate allele have to be clipped to align there, I'd say those reads are misaligned. I would say that…
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
GenoMax
142k
> Here's a few lines from the head of the raw fastq If your files are actually compressed (as their names suggest) then you should not be …
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
GenoMax
142k
If you added the `\` before the `+` then there is no need for it. It makes it appear that the sequences are not in proper fastq format. Ple…
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
Mensur Dlakic
★ 27k
This seems to be the same unanswered question as before, except that its description is split over two threads. You are now forcing us to r…
Answer: what is another word for a BLAST "hit"?
by
dec986
▴ 380
I'll probably go with "matches" even though it doesn't sound as good as just "hit"
Comment: what is another word for a BLAST "hit"?
by
bk11
★ 2.4k
> hits from BLAST hits sequences
Comment: what is another word for a BLAST "hit"?
by
Pierre Lindenbaum
161k
> is there a synonym for hits from BLAST? alignment
Comment: How are score_weights calculated in this code?
by
Ram
43k
Is this ALL the context you can give us?
Comment: Genome Assembly task + Protein Translation, assignment advice on a question
by
Ram
43k
Where did you copy-paste this from? It looks like an assignment question.
Comment: Contig assembly task, errors
by
rackbersingh
• 0
Hi Phillip, Thanks for sharing you knowledge and funnily enough this really was an amplitude test, but anyways your sharing of knowledge h…
Comment: Can I readmap short reads to rDNA references?
by
GenoMax
142k
If these are short reads and the organisms are related then you are going to have a difficult time classifying the reads.
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