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14 results • Page
1 of 1
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0
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2
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29
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Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
20 minutes ago by
Lluís R.
★ 1.2k
0
votes
0
replies
24
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
3 hours ago by
Ruqaiya
• 0
0
votes
0
replies
28
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
3 hours ago by
atharvakarkare14
▴ 10
0
votes
0
replies
37
views
What should I consider as FASTA for dataset?
PDB
FASTA
3 hours ago by
Nafi
• 0
0
votes
0
replies
31
views
Differential accessibility using DiffBinf
diffbind
5 hours ago by
Shloka
• 0
0
votes
0
replies
37
views
vg call vs vg surject
variation
graphs
6 hours ago by
aliraza3119
• 0
0
votes
0
replies
36
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
6 hours ago by
Winter
• 0
0
votes
1
reply
110
views
Finding batch and outlayers
Pca
updated 1 hour ago by
christopher medway
▴ 450 • written 11 hours ago by
Tigran
• 0
2
votes
2
replies
137
views
PDB related issue
rcsb
pdb
updated 11 hours ago by
noodle
▴ 570 • written 14 hours ago by
Nafi
• 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 5 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
0
votes
1
reply
114
views
Downloading full alignments from Pfam
pfam
updated 19 hours ago by
GenoMax
141k • written 23 hours ago by
bef1
• 0
1
vote
3
replies
233
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 17 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
1
vote
3
replies
330
views
PCA plot
DESeq2
PCAplot
updated 15 hours ago by
LauferVA
4.2k • written 4 days ago by
Aaliya
▴ 10
1
vote
6
replies
301
views
Downsampling fastq file
downsample
fastq
1 hour ago by
marco.barr
▴ 80
14 results • Page
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Recent Votes
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
which tool/software/package should I use to preprocess the rosetta-merck microarray platform raw data?
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?
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Recent Replies
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
hagl
▴ 10
Thank you very much for the response. Following your recommendation in pursuing option one by selecting highest expressions and subsequent …
Answer: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
I think it would be pertinent to use DESEq2 to perform two comparisons: the first one between the control group and condition 1, and the se…
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
Lluís R.
★ 1.2k
Many thanks for the helpful comment. Indeed, I read some of them, but I was not fully convinced and I missed the link FAQ of DESeq2. The re…
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…
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