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17 results • Page
1 of 1
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Views
Votes
Replies
2
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2.5k
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When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 4 hours ago by
zihanss
• 0 • written 23 months ago by
Vitor1
▴ 120
7
votes
7
replies
454
views
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
2 hours ago by
noodle
▴ 520
4
votes
4
replies
378
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 17 hours ago by
BioinfGuru
★ 1.7k • written 3 days ago by
Ming Tommy Tang
★ 3.9k
1
vote
6
replies
362
views
ScRNA data question
scRNA
Vlnplot
Samples
19 hours ago by
starswillfade
▴ 10
0
votes
5
replies
312
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 16 hours ago by
Istvan Albert
100k • written 3 days ago by
sehriban.buyukkilic
▴ 10
1
vote
6
replies
282
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 3 hours ago by
Jeremy Leipzig
22k • written 2 days ago by
zihanss
• 0
0
votes
2
replies
257
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 12 hours ago by
Jesse
▴ 740 • written 3 days ago by
Broccoli
• 0
0
votes
1
reply
250
views
absolute path for symbolic links in Snakefile
Snakemake
updated 12 hours ago by
Jesse
▴ 740 • written 8 days ago by
yifangt86
▴ 60
1
vote
2
replies
247
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
9 hours ago by
Francesco
▴ 10
2
votes
3
replies
240
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 13 hours ago by
Arup Ghosh
3.2k • written 1 day ago by
chaco001
▴ 40
0
votes
3
replies
227
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 6 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
O.rka
▴ 710
0
votes
2
replies
181
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
20 hours ago by
Guille
• 0
0
votes
2
replies
79
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
updated 1 hour ago by
Ram
43k • written 4 hours ago by
Ruqaiya
• 0
0
votes
0
replies
60
views
Extract protein sequence
fasta
alighment
blast
10 hours ago by
anna
▴ 20
0
votes
0
replies
59
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
9 hours ago by
tnminh89
▴ 10
0
votes
0
replies
58
views
Filter low express genes in microarray data
microarray
11 hours ago by
Chris
▴ 260
0
votes
0
replies
56
views
How to assign cell types after integration in scRNA
integration
conditions
ScRNA
seq
9 hours ago by
Francesco
▴ 10
17 results • Page
1 of 1
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
Answer: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
It takes 29 seconds to assemble this genome (20 CPUs) with the following statistics: 135 contigs, total 2821177 bp, min 200 bp, max …
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
IMO (and unfortunately) there needs to be an effort to develop these algorithms.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
Answer: How many reads for WGS Sequencing?
by
GenoMax
141k
Did you download the complete dataset available from ENA/NCBI SRA? This is an older dataset (from 2012) with a total of 1146212 reads and 1…
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller?
by
zihanss
• 0
Hello, I want to know that why my gVCF files have "./." besides "0/0", "1/1"? Thanks
Comment: gvcf joint calling
by
zihanss
• 0
![enter image description here][1] [1]: /media/images/15eedc1a-b2c6-4966-be39-b5173dab And I confused with the file that has "./." and…
Comment: gvcf joint calling
by
zihanss
• 0
![enter image description here][1] [1]: /media/images/16fd502c-4e01-4f56-8562-0e0d4aac Okay, this is the merged gVCF file.
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★ 27k
Enzymes under the umbrella of `1.1.1.-` work `with NAD(+) or NADP(+) as acceptor`. That only tells you about their cofactors, but not about…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
Comment: ScRNAseq-How to correctly choose cell type marker genes
by
Francesco
▴ 10
Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> My first question would be how strong your background in such analysis > is. Very strong. PhD+several years working in the field. > Wot…
Comment: NGS forensics: how to know if data is fabricated
by
ATpoint
82k
My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated
by
Jeremy Leipzig
22k
This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
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