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84 results • Page
2 of 2
Sort: Views
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Views
Votes
Replies
0
votes
0
replies
139
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
4 days ago by
salias
• 0
0
votes
0
replies
137
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 4 days ago by
Ram
43k • written 4 days ago by
glaciya2018
• 0
0
votes
1
reply
131
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
2
votes
2
replies
128
views
PDB related issue
rcsb
pdb
updated 7 hours ago by
noodle
▴ 550 • written 10 hours ago by
Nafi
• 0
0
votes
0
replies
119
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 4 days ago by
Ram
43k • written 4 days ago by
newuser2024
• 0
0
votes
1
reply
110
views
Downloading full alignments from Pfam
pfam
updated 15 hours ago by
GenoMax
141k • written 19 hours ago by
bef1
• 0
0
votes
0
replies
110
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
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
110
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
5 days ago by
Kash
▴ 110
0
votes
0
replies
104
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
0
replies
102
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 4 days ago by
Ram
43k • written 5 days ago by
Jeyong
• 0
0
votes
0
replies
100
views
Merging replicates from Encode project
CHIP-seq
encode
5 days ago by
Nurken
• 0
0
votes
0
replies
99
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
1 day ago by
tnminh89
▴ 10
0
votes
0
replies
98
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
5 days ago by
ohtang7
▴ 40
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
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
92
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
6 days ago by
Enrique
• 0
0
votes
0
replies
92
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 5 days ago by
Ram
43k • written 5 days ago by
SHREYA
• 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
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
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
0
votes
0
replies
85
views
Annotating single cell data automatically
cell
annotation
single
6 days ago by
Gerard
• 0
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
82
views
Finding batch and outlayers
Pca
updated 2 hours ago by
Ram
43k • written 7 hours ago by
Tigran
• 0
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
75
views
Imputation advice
imputation
6 days ago by
kl
▴ 10
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
73
views
adjusting for confounders in LMER in R
confounders
LMER
R
1 day ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
23
views
vg call vs vg surject
variation
graphs
2 hours ago by
aliraza3119
• 0
0
votes
0
replies
21
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
2 hours ago by
Winter
• 0
0
votes
0
replies
13
views
Differential accessibility using DiffBinf
diffbind
1 hour ago by
Shloka
• 0
0
votes
0
replies
11
views
What should I consider as FASTA for dataset?
PDB
FASTA
22 minutes ago by
Nafi
• 0
0
votes
0
replies
1
view
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
just now by
atharvakarkare14
▴ 10
0
votes
0
replies
1
view
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
just now by
Ruqaiya
• 0
84 results • Page
2 of 2
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
Answer: 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
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: PDB related issue
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Zhenyu Zhang
★ 1.2k
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WUSCHEL
▴ 750
Teacher
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Mensur Dlakic
★ 27k
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22k
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Recent Replies
Answer: Is it possible to bulk download files from GEO repository?
by
atharvakarkare14
▴ 10
Try using this library [GEOparse][1] [1]: https://github.com/guma44/GEOparse
Answer: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
OK. Problem solved. The problem was from my end. Thank you both for helping !!
Comment: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
Appreciate the suggestion, but that ship has sailed and reached the other shore. This happened 10+ years ago. To the best of my knowledge n…
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
Files are not opening in any of the computer (ubuntu/windows). I rereun snpEff annotation but still output html files are having missing im…
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
I reinstalled nodejs: > sudo apt-get install nodejs Its already up to date with version v10.19.0
Answer: NGS forensics: how to know if data is fabricated
by
Prash
▴ 280
Mensur, if I were you, I'd probably contact the CA directly and check with him whether they have reproduced the works recently. There coul…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 550
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
▴ 550
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…
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?
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