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116,788 results • Page
3 of 2336
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
96
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
5 days ago by
Vijith
▴ 30
9
votes
10
replies
515
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 4 days ago by
Zamin Iqbal
▴ 20 • written 5 days ago by
nicole.kavanagh
• 0
0
votes
1
reply
279
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 5 days ago by
Scooter
▴ 280 • written 11 days ago by
avocado123
• 0
0
votes
0
replies
98
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
5 days ago by
James
▴ 10
0
votes
1
reply
588
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 5 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
3
replies
239
views
Odd alignment question/finding
Alignment
updated 3 days ago by
barslmn
★ 2.1k • written 5 days ago by
poordumbsillyidiot
• 0
0
votes
1
reply
207
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 5 days ago by
GenoMax
142k • written 5 days ago by
mgranada3
▴ 30
0
votes
0
replies
98
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
5 days ago by
meck
• 0
0
votes
0
replies
124
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 5 days ago by
Ram
43k • written 5 days ago by
Oscar
▴ 10
0
votes
7
replies
554
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 4 days ago by
LChart
3.9k • written 7 days ago by
kl
▴ 10
0
votes
1
reply
222
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 5 days ago by
Adam
▴ 30 • written 6 days ago by
J
• 0
1
vote
3
replies
309
views
DESeq2 processing problems
deseq2
R
updated 5 days ago by
ATpoint
82k • written 5 days ago by
jagdish7921
• 0
0
votes
1
reply
782
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 4 days ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
151
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 5 days ago by
Ram
43k • written 5 days ago by
ernestine.kubi
• 0
0
votes
0
replies
106
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
5 days ago by
VITALA
• 0
1
vote
2
replies
252
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
5 days ago by
rianna.collins
• 0
0
votes
1
reply
186
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 5 days ago by
i.sudbery
19k • written 6 days ago by
Edmond
• 0
0
votes
0
replies
145
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
6 days ago by
O.rka
▴ 710
0
votes
1
reply
681
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 6 days ago by
Ram
43k • written 6 days ago by
Dr Huma Naz
• 0
2
votes
2
replies
275
views
p-value in CIBERSORT
CIBERSORT
p-value
5 days ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
377
views
Telescope issue
Telescope
RNA-seq
updated 5 days ago by
GenoMax
142k • written 6 days ago by
eleven11
• 0
5
votes
6
replies
525
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 6 days ago by
me
▴ 760 • written 7 days ago by
Mariana
▴ 40
1
vote
1
reply
234
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 6 days ago by
Ram
43k • written 6 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
292
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
5 days ago by
Nafi
• 0
1
vote
3
replies
282
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 6 days ago by
GenoMax
142k • written 6 days ago by
jeffrey.maurer.informatics
• 0
1
vote
3
replies
280
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
1 day ago by
Dora
▴ 10
0
votes
0
replies
166
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 6 days ago by
Ram
43k • written 6 days ago by
Chakri
• 0
0
votes
1
reply
189
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 5 days ago by
Adam
▴ 30 • written 6 days ago by
Ahiad Chen Zion
• 0
1
vote
5
replies
332
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
3 days ago by
Riccardo
▴ 10
0
votes
0
replies
138
views
barcode of TCR-sequencing
barcode
6 days ago by
yueli7
▴ 250
0
votes
0
replies
130
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 6 days ago by
Ram
43k • written 6 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
127
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 6 days ago by
Ram
43k • written 6 days ago by
Alexandros
• 0
0
votes
1
reply
175
views
unable to get feature count results
featureCounts
updated 6 days ago by
Ram
43k • written 6 days ago by
Ravita
• 0
0
votes
3
replies
287
views
KEGG Pathways
r
RNA-seq
updated 6 days ago by
Ram
43k • written 6 days ago by
Sudip
• 0
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 6 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
135
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
6 days ago by
Bine
▴ 60
0
votes
1
reply
290
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
6 days ago by
David Langenberger
11k
0
votes
1
reply
192
views
Deseq2
Deseq2
updated 6 days ago by
Jack Tierney
▴ 360 • written 6 days ago by
Sudip
• 0
1
vote
1
reply
235
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 6 days ago by
Michael
54k • written 7 days ago by
Lissa Cruz Saavedra
• 0
5
votes
3
replies
283
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 6 days ago by
Lluís R.
★ 1.2k • written 7 days ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
202
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 6 days ago by
ATpoint
82k • written 6 days ago by
Sudip
• 0
1
vote
2
replies
229
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 6 days ago by
Ram
43k • written 6 days ago by
Ravita
• 0
2
votes
2
replies
186
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
updated 17 hours ago by
GenoMax
142k • written 6 days ago by
Adyasha
• 0
0
votes
0
replies
116
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
7 days ago by
fanglujing
▴ 60
0
votes
0
replies
134
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
7 days ago by
Jacob
• 0
0
votes
3
replies
745
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 7 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
277
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 7 days ago by
Ram
43k • written 7 days ago by
Hamtaro
▴ 50
0
votes
1
reply
183
views
Differential Accessibility
DiffBind
updated 7 days ago by
Ram
43k • written 7 days ago by
Shloka
• 0
0
votes
3
replies
294
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 6 days ago by
GenoMax
142k • written 7 days ago by
kim
• 0
3
votes
2
replies
385
views
Extract protein sequence
fasta
alignment
blast
6 days ago by
anna
▴ 20
116,788 results • Page
3 of 2336
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Answer: ATAC-Seq and RPKM
Answer: MSA and distance matrix in R
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Comment: Which hg38 file?
Answer: Which hg38 file?
Answer: Where to get the following bed file?
How to save GRanges object to csv file
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Answer: Bioinformatics Analyst - Laboratory Medicine and Pathology
by
Xiaofen
• 0
I'm having a problem and I can't find the button to post, how do you post?
Comment: We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
by
MICOS
• 0
Contest question details: **To effectively address the accuracy and efficiency issues of clustering algorithms used for spatial transcript…
Comment: HCL database download
by
sooni
▴ 20
I would like to download top markers for each subpopulation data. Is there no way? It seems different from the DGE data.
Comment: Understanding STAR output (Aligned.out.sam file)
by
GenoMax
142k
Refer to SAM alignment format: https://samtools.github.io/hts-specs/SAMv1.pdf Check section 1.4.
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3.9k
Step 1: Go to TCGA in the GDC and open the Cohort Builder https://portal.gdc.cancer.gov/analysis_page?app=CohortBuilder&tab=general Step …
Comment: Where to get the following bed file?
by
GenoMax
142k
SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
Answer: Where to get the following bed file?
by
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3.9k
UCSC maintains a list of exome probe sets and targets. You could check there: https://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
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by
Ngrin
• 0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
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bk11
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Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
Answer: How to compute TPM normalized values for TCGA miRNA data?
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dsull
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TPM is irrelevant for miRNA-seq; CPM works fine. TPM tries to adjust for length effects by dividing by gene length (e.g. reducing the im…
Comment: Applying the metacell2 algorithm using python
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"I'm also unsure what qualifies as a lateral gene." The [README where you reference](https://metacells.readthedocs.io/en/latest/readme.htm…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
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sovrappensiero
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Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
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Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
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