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79 results • Page
2 of 2
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1
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1
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175
views
Failed kmer content
kmer
illumina
ngs
updated 5 days ago by
Ram
43k • written 5 days ago by
Kasturi
• 0
0
votes
0
replies
87
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 5 days ago by
Ram
43k • written 6 days ago by
SSSJec
• 0
0
votes
1
reply
147
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 6 days ago by
Ram
43k • written 6 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
335
views
Error in cnetplot enrichplot package
R
updated 6 days ago by
Ram
43k • written 6 days ago by
Farhad
• 0
0
votes
0
replies
110
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 6 days ago by
Ram
43k • written 6 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
93
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 6 days ago by
Ram
43k • written 6 days ago by
sansan_96
▴ 80
0
votes
0
replies
97
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 5 days ago by
Ram
43k • written 6 days ago by
Amélie
• 0
0
votes
0
replies
199
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 6 days ago by
Ram
43k • written 6 days ago by
Oak
▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 6 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
5
replies
284
views
Downsampling fastq file
downsample
fastq
updated 6 days ago by
Ram
43k • written 6 days ago by
marco.barr
▴ 80
0
votes
1
reply
139
views
tbtool
tbtool
updated 6 days ago by
Ram
43k • written 6 days ago by
Raman
• 0
0
votes
7
replies
331
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
GenoMax
141k • written 6 days ago by
Patadu94
• 0
0
votes
1
reply
130
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 6 days ago by
ATpoint
82k • written 6 days ago by
enanoide
• 0
0
votes
0
replies
89
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
6 days ago by
manaswwm
▴ 510
0
votes
0
replies
80
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
5 days ago by
alifafiq1
• 0
0
votes
0
replies
86
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
6 days ago by
feather-W
• 0
2
votes
4
replies
287
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
4 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
85
views
Annotating single cell data automatically
cell
annotation
single
6 days ago by
Gerard
• 0
0
votes
1
reply
157
views
RNA-seq bacteria contamination
RNA-seq
updated 6 days ago by
GenoMax
141k • written 6 days ago by
sh
• 0
0
votes
0
replies
74
views
Imputation advice
imputation
6 days ago by
kl
▴ 10
0
votes
0
replies
92
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
6 days ago by
Enrique
• 0
0
votes
0
replies
75
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
6 days ago by
sativus
▴ 20
0
votes
0
replies
82
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
6 days ago by
Biostars2200
• 0
0
votes
0
replies
133
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 6 days ago by
Carlo Yague
8.7k • written 7 days ago by
Atul K.
• 0
2
votes
5
replies
459
views
Marking duplicates using UMIs
Deduplication
UMI
updated 6 days ago by
i.sudbery
19k • written 8 days ago by
Lipika
• 0
0
votes
0
replies
206
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
6 days ago by
Javier
• 0
1
vote
2
replies
241
views
permutation test in edgeR
rna-seq
edgeR
updated 6 days ago by
Gordon Smyth
★ 7.0k • written 20 days ago by
Netanel
• 0
0
votes
6
replies
443
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 4 days ago by
gv
• 0 • written 27 days ago by
Srinka
▴ 20
0
votes
0
replies
275
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 6 days ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
79 results • Page
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Recent Votes
Comment: NGS forensics: how to know if data is fabricated
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
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Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 540
Working on it - it's actually a bit difficult. Low coverage of ribosomal proteins. Low coverage of housekeeping genes ...I'm trying to find…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 540
I'm a bit against pubpeer - have you ever posted there? My gripe with them is that the posts are heavily moderated and EDITED to the point…
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
Thanks Mensur! I'd add that in 9 out of 10 cases, you won't receive a reply to a request for raw data. That's just how scientists are, does…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
I had downloaded the two files in a similar manner actually.
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
ok, i'll try to use fastp. I have only used trimmomatic and cutadapt till now and they dont identify on its own. Except the graph in fastqc…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
got it! even if i'm doing the assembly for paired end with both the files do i have set the threshold to 1000bp ?
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
by
Gordon Smyth
★ 7.0k
> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
Answer: Finding batch and outlayers
by
Tigran
• 0
![enter image description here][1] [1]: /media/images/aa60b9ef-b08c-4093-9f0d-fb656a5c
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
Comment: PDB related issue
by
noodle
▴ 540
You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
Comment: PDB related issue
by
Mensur Dlakic
★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
Answer: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
I downloaded the data in two files from the link you provided. With this command: megahit -1 ERR072246_1.fastq.gz -2 ERR072246_2.fastq…
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