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24 results • Page
1 of 1
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Views
Votes
Replies
0
votes
3
replies
714
views
to annotate BEDPE files
bedtools
annotate
updated 18 hours ago by
Lhl
▴ 760 • written 2.6 years ago by
Bogdan
★ 1.4k
13
votes
16
replies
541
views
ncbi error report log for validate fastq issue
sra-tools
updated 6 hours ago by
GenoMax
134k • written 19 hours ago by
1769mkc
★ 1.1k
4
votes
6
replies
355
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
updated 22 hours ago by
Istvan Albert
98k • written 4 days ago by
Athena
• 0
0
votes
4
replies
259
views
How to determine the total count for each gene in lymphotype B
scRNAseq
Seurat
11 hours ago by
dalibenam64
• 0
0
votes
4
replies
214
views
Troubles launch IGV on Linux(Debian)
IGV
6 hours ago by
PoscaXVIII
• 0
0
votes
4
replies
182
views
Sequence quality drops in the 3' end of the left sequence in paired end. What could be the cause?
sequencing
updated 14 hours ago by
GenoMax
134k • written 18 hours ago by
eggrandio
▴ 40
1
vote
4
replies
154
views
How to filter vcf file by MAF using bcftools?
bcftools
vcf
updated 10 hours ago by
Ram
40k • written 11 hours ago by
_quantum_girl_
▴ 10
4
votes
4
replies
146
views
Software Tool to Translate DNA to Protein
protein
DNA
fasta
updated 10 hours ago by
Ram
40k • written 11 hours ago by
sperezilvia
• 0
0
votes
3
replies
141
views
Bug of vg surject
vg
updated 22 hours ago by
Jordan M Eizenga
▴ 360 • written 23 hours ago by
Qi
• 0
1
vote
4
replies
128
views
CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM
R
Picard
CollectRnaSeqMetrics
4 hours ago by
camillab.
▴ 140
0
votes
1
reply
121
views
GO ENRICHMENT ANALYSIS- DESEQ
GO
updated 19 hours ago by
Basti
★ 1.7k • written 1 day ago by
oduduabasi.isaiah
• 0
0
votes
1
reply
114
views
Calculating haplotype and nucleotide diversity with deep amplicon sequencing data
haplotype
diversity
Pegas
Arlequin
HTS_data
16 hours ago by
deorugz
• 0
0
votes
2
replies
103
views
What is the correct procedure to generate a consensus bacterial sequence?
consensus
samtools
illumina
fastq
updated 9 hours ago by
Istvan Albert
98k • written 12 hours ago by
marongiu.luigi
▴ 690
0
votes
2
replies
101
views
Github access with token headache
Github
git
updated 10 hours ago by
Ram
40k • written 12 hours ago by
Begonia_pavonina
▴ 100
0
votes
1
reply
81
views
Detect STRs in illumina library
repeats
annotation
STR
updated 11 hours ago by
bk11
★ 1.2k • written 14 hours ago by
kirillkirilenko
▴ 20
0
votes
1
reply
75
views
Frustrated with DEA results
microarray
differential-expression
updated 5 hours ago by
dsull
★ 4.7k • written 8 hours ago by
jopadrosa
• 0
0
votes
1
reply
64
views
Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
R
edgeR
limma
RNA-seq
updated 3 hours ago by
LChart
3.4k • written 5 hours ago by
svlachavas
▴ 780
0
votes
2
replies
56
views
Network analysis with cytoscape
RNA-seq
cytoscape
1 hour ago by
Chris
▴ 180
0
votes
0
replies
51
views
Get support value of MRCA given a list of tip.label in R newick trees
phylogeny
newick
R
ape
tree
13 hours ago by
pl.terzian
• 0
0
votes
0
replies
45
views
How to obtain de pvalue of my DMRs using Bumphunter function from minfi
DMRs
11 hours ago by
Irene
• 0
0
votes
0
replies
42
views
Obtain gene disease association from DisGeNET
DisGeNET
genes
disease
11 hours ago by
ThePlaintiff
▴ 80
0
votes
0
replies
40
views
Select minimum set of SNPs from VCF file to identify a individual
selection
SNP
9 hours ago by
Bioxbio
• 0
0
votes
0
replies
17
views
tensorQTL interaction issue
genomics
eqtl
genetics
qtl
2 hours ago by
Solal
• 0
0
votes
0
replies
13
views
comparision of umap single cell
singlecell
1 hour ago by
synat.keam
▴ 80
24 results • Page
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Recent Votes
Comment: demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_stran
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Updated List of Unix tutorials 2023
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Recent Replies
Answer: Have some issues in running prokka on WSL
by
Philipp Bayer
7.9k
It looks like the conda-installed BLAST has issues with the system's ZSTD, which is probably some WSL weirdness. You *might* be able to fix…
Comment: Network analysis with cytoscape
by
Chris
▴ 180
Sure, the network represents the different expressed genes in my RNA-seq. I choosed string protein query.
Comment: Network analysis with cytoscape
by
Yogi
▴ 40
A few questions. 1. What does the network represent? 2. Can you insert a high level picture of the network (or pictures) if you want to zo…
Answer: Chip-Seq and correlation of bam file
by
jared.andrews07
★ 15k
Use [deepTools' plotCorrelation function](https://deeptools.readthedocs.io/en/develop/content/tools/plotCorrelation.html).
Answer: Transcription factor co-localization p-values
by
jared.andrews07
★ 15k
[regioneR](https://bioconductor.org/packages/release/bioc/html/regioneR.html) seems to be what you want.
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
by
LChart
3.4k
> Our major biological questions are: to have a general comparison of cancer vs normal “treatment” conditions; In addition if doable, to co…
Comment: Which function is best for pathway analysis?
by
Chris
▴ 180
Thanks @luffy! Great material but seem they didn't mention how to customize the background genes depend on our data.
Comment: CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM
by
camillab.
▴ 140
I have calculate from this [tutorial][1]. so basically it retrieve the normalized counts matrix using `Deseq2` . Do you think it is correct…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore
by
GenoMax
134k
`dorado` can't demultiplex data as yet (v.0.3.4). Also no adapter trimming. So something to keep in mind if you are switching. To address …
Comment: Frustrated with DEA results
by
dsull
★ 4.7k
Let the data speak. If there's no difference, then there's no difference. Human clinical data is always messy and unpredictable, especiall…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore
by
Ram
40k
I don't think they bought the Mac Studio just for the MiniON. If they did, that might be overkill. All things considered, I'd prefer an App…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore
by
ATpoint
77k
Wondering why investing all that money for such an overpriced piece of hardware. You could get an equivalent Windows or Linux workstation f…
Answer: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore
by
Christopher
▴ 10
I'm using a Mac Studio with M1 Ultra chip to sequence with a MinION Mk1B now and it's working great! Fast basecalling and adaptive sequenci…
Comment: ncbi error report log for validate fastq issue
by
GenoMax
134k
You may want to use `--split-files` instead. With your `--split-spot` option looks like you end up with interleaved data files. Unless you …
Comment: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
by
Ram
40k
Nope, I kinda gave up. I got to the image on what fragment size is (https://www.biostars.org/p/106291/#106344) but cannot figure out how to…
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