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20 results • Page
1 of 1
Sort: Views
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Views
Votes
Replies
0
votes
1
reply
536
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 11 hours ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
0
votes
5
replies
311
views
Telescope issue
Telescope
RNA-seq
updated 21 hours ago by
GenoMax
142k • written 1 day ago by
eleven11
• 0
1
vote
2
replies
200
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
8 hours ago by
rianna.collins
• 0
0
votes
1
reply
159
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 19 hours ago by
Adam
▴ 30 • written 2 days ago by
Ahiad Chen Zion
• 0
0
votes
1
reply
151
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 12 hours ago by
GenoMax
142k • written 16 hours ago by
mgranada3
▴ 30
0
votes
1
reply
151
views
Subsetting and merging back Seurat Object brings different results
Seurat
1 hour ago by
Bine
▴ 60
1
vote
2
replies
118
views
Odd alignment question/finding
Alignment
updated 5 hours ago by
ATpoint
82k • written 11 hours ago by
poordumbsillyidiot
• 0
0
votes
1
reply
98
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 20 hours ago by
Ram
43k • written 22 hours ago by
ernestine.kubi
• 0
0
votes
4
replies
78
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 57 minutes ago by
GenoMax
142k • written 3 hours ago by
Begonia_pavonina
▴ 150
0
votes
0
replies
78
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 15 hours ago by
Ram
43k • written 17 hours ago by
Oscar
▴ 10
0
votes
0
replies
69
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
22 hours ago by
VITALA
• 0
0
votes
1
reply
67
views
How to perform single cell multimodal integration using Seurat for Geo datasets
cell
analysis
multimodal
single
updated 6 hours ago by
ATpoint
82k • written 7 hours ago by
nithya
• 0
1
vote
1
reply
65
views
Discrepancy in read counts from fastq
reads
downsampling
fastq
count
updated 2 hours ago by
GenoMax
142k • written 5 hours ago by
marco.barr
▴ 90
0
votes
0
replies
55
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
17 hours ago by
meck
• 0
0
votes
0
replies
47
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
10 hours ago by
James
▴ 10
0
votes
0
replies
42
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
8 hours ago by
Jeol
▴ 20
0
votes
0
replies
40
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
8 hours ago by
Vijith
▴ 30
0
votes
0
replies
34
views
Super ehancers
enhancers
3 hours ago by
Oburah
• 0
0
votes
0
replies
31
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
5 hours ago by
Rhiannon
• 0
0
votes
0
replies
27
views
Use of annotation of integrated Seurat object in single sample
Seurat
3 hours ago by
Bine
▴ 60
20 results • Page
1 of 1
Recent Votes
A: What is the difference between GRCh37 and hs37? And hg19?
A: Decoy In Reference Assembly
A: Decoy In Reference Assembly
Decoy In Reference Assembly
Decoy In Reference Assembly
Comment: Bacterial plasmid analysis
Unsupervised clustering on gene expression data
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Recent Replies
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
GenoMax
142k
Use `vdb-validate` included in `sratoolkit` to check your `*.sra` files for integrity.
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
ATpoint
82k
This `fastq-dump --split-files *.sra` gives you fastq files. I am not sure how, with the given information, one might debug your problem. A…
Answer: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
DESeq2 has a "lessAbs" test which gioves you a pvalue that tests whether a fold change is **below** a user-defined threshold, see https://b…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
In your table RawCounts, keep only the columns corresponding to condition 1 and the control. Edit the table sampleTable to align with your …
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
Begonia_pavonina
▴ 150
Thank you @atpoint, I did already investigate this error on the DADA2 github. It seems that the "BiocParallel" error can be due to multipl…
Comment: Discrepancy in read counts from fastq
by
GenoMax
142k
Try `reformat.sh` from BBMap suite and its sampling parameters. You may get a third answer. Programs do some approximations so it is probab…
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
ATpoint
82k
One cannot help you with this. The error is from R, yet you show not a single line of R code.
Comment: Bacterial plasmid analysis
by
Daria
▴ 10
I am the colleague! My tool groups together plasmids based on two genetic distances: containment (how much of the smaller plasmid's sequenc…
Comment: Subsetting and merging back Seurat Object brings different results
by
Bine
▴ 60
Ok I think I know what happened. The order of cells changed, otherwise its the same: ![image](https://github.com/satijalab/seurat/assets/7…
Answer: Bacterial plasmid analysis
by
shenwei356
8.5k
My colleague has an unpublished tool for plasmid analysis (clustering), and it has really good results. You might have a try. https://githu…
Comment: Odd alignment question/finding
by
ATpoint
82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
Comment: How to perform single cell multimodal integration using Seurat for Geo datasets
by
ATpoint
82k
It's funny that you ask because the paper that these data were used for is called `Integrated analysis of multimodal single-cell data` from…
Comment: Odd alignment question/finding
by
liorglic
★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
Answer: Bacterial plasmid analysis
by
Mensur Dlakic
★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
Comment: POSSUM not working due to incompatible pssm file
by
rianna.collins
• 0
Thank you so much. I'm new to this and didn't realise there was a code option.
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