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27 results • Page
1 of 1
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33
votes
20
replies
1.2k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 1 hour ago by
i.sudbery
19k • written 1 day ago by
noodle
▴ 570
5
votes
16
replies
494
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
2 hours ago by
Ruqaiya
• 0
2
votes
2
replies
211
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 53 minutes ago by
i.sudbery
19k • written 2 days ago by
vanbelj
▴ 40
2
votes
5
replies
388
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
15 hours ago by
ashaneev07
▴ 20
2
votes
7
replies
1.2k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 9 hours ago by
Gordon Smyth
★ 7.0k • written 8 months ago by
Calum
▴ 10
2
votes
5
replies
299
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
3 hours ago by
analyst
▴ 30
2
votes
2
replies
136
views
PDB related issue
rcsb
pdb
updated 10 hours ago by
noodle
▴ 570 • written 13 hours ago by
Nafi
• 0
2
votes
11
replies
769
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 12 minutes ago by
jkbonfield
★ 1.2k • written 11 days ago by
me
• 0
1
vote
3
replies
330
views
PCA plot
DESeq2
PCAplot
updated 14 hours ago by
LauferVA
4.2k • written 4 days ago by
Aaliya
▴ 10
1
vote
3
replies
325
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 13 hours ago by
Mensur Dlakic
★ 27k • written 2 days ago by
O.rka
▴ 710
1
vote
3
replies
232
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 15 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
1
vote
6
replies
296
views
Downsampling fastq file
downsample
fastq
28 minutes ago by
marco.barr
▴ 80
0
votes
1
reply
102
views
Finding batch and outlayers
Pca
updated 38 minutes ago by
christopher medway
▴ 450 • written 9 hours ago by
Tigran
• 0
0
votes
0
replies
65
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
30 minutes ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
705
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 22 hours ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
0
votes
1
reply
15
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
updated 12 minutes ago by
ATpoint
82k • written 30 minutes ago by
Lluís R.
★ 1.2k
0
votes
1
reply
112
views
Downloading full alignments from Pfam
pfam
updated 18 hours ago by
GenoMax
141k • written 22 hours ago by
bef1
• 0
0
votes
0
replies
35
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
5 hours ago by
Winter
• 0
0
votes
0
replies
36
views
vg call vs vg surject
variation
graphs
4 hours ago by
aliraza3119
• 0
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 4 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
0
votes
0
replies
30
views
Differential accessibility using DiffBinf
diffbind
4 hours ago by
Shloka
• 0
0
votes
0
replies
27
views
What should I consider as FASTA for dataset?
PDB
FASTA
2 hours ago by
Nafi
• 0
0
votes
1
reply
60
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 2 hours ago by
atharvakarkare14
▴ 10 • written 4 hours ago by
WUSCHEL
▴ 750
0
votes
0
replies
17
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
2 hours ago by
atharvakarkare14
▴ 10
0
votes
0
replies
17
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
2 hours ago by
Ruqaiya
• 0
0
votes
5
replies
205
views
What does it mean single base resolution in sequencing?
SNP
sequencing
2 hours ago by
jinyu
▴ 10
0
votes
1
reply
34
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 1 hour ago by
i.sudbery
19k • written 1 hour ago by
DOBI
• 0
27 results • Page
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Recent Votes
Answer: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
NGS forensics: how to know if data is fabricated
Answer: ChIP-seq datasets: input samples omitted?
Comment: 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
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
ATpoint
82k
Keeping data together is most powerful and most convenient as you have a single analysis object and a single count matrix. I would always d…
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
Assuming you have network access and the md5sum is registered with the EBI's reference server, yes - it'll be downloaded and cached locally.
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I followed your advice and it seems that I'm getting results comparable to what I was getting before. Upon checking with `wc -l` on the ori…
Comment: Finding batch and outlayers
by
christopher medway
▴ 450
You could perform an ANOVA to test if there is a significant association between batch number and a given Principal Component
Comment: ChIP-seq datasets: input samples omitted?
by
i.sudbery
19k
Fascinating! We also use inputs when doing metagene to protect against those situations where regions up or downstream of our metagene al…
Answer: How to solve DESeq2 Error in checkFullRank(modelMatrix)?
by
i.sudbery
19k
See the section on non full rank design matrices in the DESeq2 manual. In this case your problem is that healthy and 0dpi samples are e…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
Can you clarify what you mean by "100% of reads pass cutadapt, even though 70% of reads contain adapters and get trimmed. " did you set a m…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
I don't follow your argument for distinguishing between genomic contamination and freud. A data set being bad in terms of genomic contamin…
Comment: What does it mean single base resolution in sequencing?
by
jinyu
▴ 10
Thank you for your detail and great explanation. I do need more time to understand these. And there is still something compuzzling me. For …
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…
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