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158 results • Page
2 of 4
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Votes
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0
votes
1
reply
170
views
Information on sequin RNA spike in standards
Sequin
Spike-in
RNA-seq
updated 1 day ago by
ATpoint
72k • written 3 days ago by
akainth
▴ 10
1
vote
9
replies
355
views
Trying to edit VCF file
VCF
R
bcftools
snpsaurus
updated 3 days ago by
Ram
39k • written 3 days ago by
peavy
• 0
0
votes
1
reply
388
views
How to quantification proteomics data
proteomics
updated 3 days ago by
eqoa45
• 0 • written 19 months ago by
LeeLee
▴ 10
1
vote
4
replies
241
views
Is hg38 on the multiz 30-way alignment inaccurate?
maf
UCSC
PHAST
multiz
3 days ago by
Daniel
▴ 30
0
votes
2
replies
1.5k
views
How to perform statistical analysis of label free experiment using results from Proteome Discoverer?
Proteome-Discoverer
Label-Free
Proteomics
updated 3 days ago by
Ram
39k • written 4.5 years ago by
k2bhide
▴ 80
0
votes
0
replies
114
views
Label free quantification in Proteome discoverer software
proteomics
quantification
spectrometry
shotgun
3 days ago by
eqoa45
• 0
1
vote
0
replies
114
views
How to predict gene amplification from RNAseq and ATACseq data?
amplification
ATAC
3 days ago by
Dan
▴ 120
1
vote
2
replies
190
views
hisat2 Error 137
hisat2
RNA-seq
3 days ago by
Forough
▴ 10
0
votes
1
reply
167
views
Error occured at the PHG imputation step: allele in genotype not in the variant context
PHG
Imputation
PracticalHaplotypeGraph
Haplotype
updated 15 hours ago by
lcj34
▴ 230 • written 3 days ago by
xeod21
• 0
3
votes
6
replies
365
views
Embryo transcriptome
database
transcriptome
SRA
updated 1 day ago by
Basti
★ 1.6k • written 3 days ago by
firefox91
• 0
1
vote
3
replies
200
views
Obtain a --gene-trans-map file after rnaSPAdes
rnaSPAdes
Trinity
3 days ago by
UserA
• 0
0
votes
0
replies
92
views
How to extract only neutral markers from low-coverage whole genome sequencing?
low-coverage
whole-genome-sequencing
updated 3 days ago by
Ram
39k • written 3 days ago by
beausoleilmo
▴ 530
0
votes
4
replies
228
views
Difference between USCS exon coordinates and ensembl
exons
Ensembl
3 days ago by
amy__
▴ 50
0
votes
0
replies
93
views
Why sone miRNAs are not present in TCGA data
TCGA
miRNA
RNA-seq
3 days ago by
nicolo.gualandi
• 0
0
votes
0
replies
86
views
Prediction of altrered metabolites from altered gene expression
Gene
Metabolites
3 days ago by
english.server
▴ 290
0
votes
6
replies
366
views
variant allelic fraction
vep
updated 2 days ago by
Ram
39k • written 4 days ago by
Jom
• 0
0
votes
1
reply
155
views
Pairwise Alignment
Pairwise-Alignment
updated 3 days ago by
Ram
39k • written 4 days ago by
Fatemeh
• 0
0
votes
0
replies
99
views
How to perform a phylogenetic analysis from a vcf file
variants
haplotyping
phylogeny
vcf
4 days ago by
rj.rezwan
• 0
0
votes
1
reply
169
views
Where to get the molecular subtype information of STAD sample in TCGA
TCGA
database
updated 4 days ago by
Hamid Ghaedi
2.9k • written 4 days ago by
younglin113
▴ 50
0
votes
0
replies
137
views
How to keep ComplexHeatmap from reordering annotations
Dendrogram
HeatmapAnnotations
R
Heatmap
ComplexHeatmap
5 days ago by
Manuel
• 0
2
votes
3
replies
254
views
Differential protein expression analysis
R
proteomic
statistics
updated 1 day ago by
dsull
★ 4.2k • written 5 days ago by
Ribo
▴ 40
0
votes
3
replies
334
views
(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
bowtie2
align_stats
trinity
4 days ago by
eimanpharmacist
▴ 20
0
votes
4
replies
380
views
What are recommended parameters for the local protein alignment ?
protein
alignment
4 days ago by
Alexander
▴ 100
0
votes
0
replies
134
views
microsatellite, SSR, using Galaxy
Galaxy
SSR
using
microsatellite
5 days ago by
m.esmaeilpour
▴ 10
0
votes
0
replies
148
views
decoupleR & Transcription Factory Activity Inference: pvalue or padj?
pvalue
padj
decoupleR
6 days ago by
OST
▴ 10
2
votes
3
replies
346
views
Low mapping percentage
mapping
STAR
RNAseq
5 days ago by
Sib
▴ 40
0
votes
0
replies
177
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential
visualization
RNASeq
analysis
expression
enrichment
6 days ago by
Mark
• 0
0
votes
0
replies
162
views
busco id description
OrthoDB
BUSCO
updated 6 days ago by
Ram
39k • written 6 days ago by
angelina
• 0
0
votes
5
replies
400
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 6 days ago by
Joe
21k • written 6 days ago by
gunala.nikhil
• 0
0
votes
0
replies
164
views
NMDS plotting issue
NMDS
metagenomic
6 days ago by
arshad1292
▴ 90
0
votes
2
replies
250
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
3 days ago by
demoraesdiogo2017
▴ 90
0
votes
0
replies
143
views
IGV insertions
insertions
IGV
6 days ago by
christoph.schubart
• 0
1
vote
0
replies
163
views
Bayesian network for biological data using bnlearn
bnlearn
RNA-seq
bayesian-network
updated 6 days ago by
Ram
39k • written 6 days ago by
priyankamehta.1811
▴ 10
0
votes
0
replies
150
views
jellyfish options
kmer
jellyfish
6 days ago by
Tele
• 0
0
votes
3
replies
231
views
hardfilter error
bam
recall
6 days ago by
bestone
▴ 10
0
votes
0
replies
127
views
cnetplot enrichment graph to cytoscape
clusterprofiler
cnetplot
enrichplot
6 days ago by
Omics data mining
▴ 220
0
votes
0
replies
126
views
How to extract the surrogate variables from DNA methlation Data
sva
array
limma
methylation
updated 6 days ago by
GenoMax
130k • written 6 days ago by
Dablax
• 0
1
vote
1
reply
608
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 6 days ago by
GenoMax
130k • written 6 days ago by
Mohd
▴ 20
0
votes
0
replies
119
views
Convert tree into bifurcation table
Tree
Newick
ASR
Mutation
6 days ago by
Alexandre
• 0
0
votes
1
reply
193
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
updated 6 days ago by
raphael.B
▴ 360 • written 6 days ago by
sonsunjirachote
• 0
1
vote
2
replies
235
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 6 days ago by
thadjudkins2
• 0 • written 7 days ago by
herh
• 0
4
votes
5
replies
340
views
Does adding reads cause batch effects?
kallisto
RNAseq
15 hours ago by
bioinfo
▴ 80
0
votes
1
reply
167
views
Merge different vcf files
vcf
updated 6 days ago by
Ram
39k • written 7 days ago by
caique.manochio
• 0
0
votes
8
replies
355
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 6 days ago by
GenoMax
130k • written 7 days ago by
Marta
• 0
1
vote
2
replies
211
views
Combination of ROC CURVE
roccurve
R
AUC
4 days ago by
Maria17
▴ 20
2
votes
2
replies
184
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
analysis
CD
Protocol
updated 2 days ago by
Ram
39k • written 8 days ago by
linnet.roque6
▴ 10
0
votes
2
replies
307
views
too many zeros in 16S rRNA amplicon sequencing data
16S
rRNA
2 days ago by
zhangdengwei
▴ 190
0
votes
2
replies
199
views
Samtools index and sambamba-depth error?
linux
samtools
indexing
sambamba
updated 19 hours ago by
jkbonfield
★ 1.0k • written 15 days ago by
MobiusT
▴ 10
0
votes
2
replies
238
views
[python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must be integers)
TypeError
python
offtopic
updated 1 day ago by
Ram
39k • written 7 weeks ago by
probioquestioner
• 0
0
votes
0
replies
269
views
fragments.tsv.gz file in ATAC seq
ATAC-seq
updated 1 day ago by
Ram
39k • written 9 weeks ago by
Chris
▴ 100
158 results • Page
2 of 4
Recent Votes
A: Why so many biomarkers based classifiers claim high accuracy but rare used in cl
A: Why so many biomarkers based classifiers claim high accuracy but rare used in cl
Comment: UCSC genome browser
Answer: Downloading "dbsnp 146.hg38.vcf.gz" file for BQSR
Downloading "dbsnp 146.hg38.vcf.gz" file for BQSR
Answer: Creating a local version of Clustered NR database
Comment: Filtering genes after TPM normalization
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▴ 40
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▴ 60
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• 0
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Recent Replies
Answer: No @hd header returned in sam file when running bwa mem
by
GokalpC
▴ 80
Your sam file is not coordinate sorted or converted to a bam. @HD tags come after a secondary tool such as samtools view or sort. ANGSD…
Comment: Mapping a predicted sequence to a genome
by
Mensur Dlakic
★ 23k
It may or may not, depending on the exact organism. For example, baker's yeast has introns but not many, and most genes in its genome don't…
Comment: Mapping a predicted sequence to a genome
by
Andy
• 0
Thank you for your answer! If the organism I am studying has introns, will blastn still be sufficient?
Answer: Mapping a predicted sequence to a genome
by
Mensur Dlakic
★ 23k
If we are talking about organisms without introns, it is very simple. A tool to use is `tblastn` which can be accessed from the [**main BLA…
Comment: How to get information about promoter from bulk-RNAseq?
by
rfran010
▴ 170
I'll just add what I did with my own dataset of ribo depleted RNA-seq: I took predicted enhancer-promoter interaction datasets from UCSC a…
Answer: How to get information about promoter from bulk-RNAseq?
by
rfran010
▴ 170
What type of RNA-seq data do you have? With polyA, I think it will be hard to incorporate enhancer info without additional datasets. …
Comment: Reorder GO terms using R
by
hellokwmin
• 0
Thank you so much. It worked perfectly.
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
Thank you so much, Gordon!
Comment: Help with running ATAC using Encode pipeline
by
rfran010
▴ 170
Yes, it is a lot to take in. In your input json, is "atac.fastqs_wt_rep2_R2" valid? This key should match exactly what is given in the exa…
Comment: How to calculate TPM from featureCounts output
by
rfran010
▴ 170
Yes, I thought the featureCounts file is your counts file.
Comment: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
The code should be: ``` library(edgeR) group<- factor(type) design <- model.matrix(~group) mrna.dge <- DGEList(counts=mat, group=group) ke…
Comment: If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam fil
by
javiflaja
• 0
1) I realised I was supposed to add RGs during alingment command only after I was long done with that step. But I imgined the tool "addorre…
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴ 260
Thanks @genomax > This seems reasonable since it should capture significant part of sequence to search against ( 90% identity and 90% …
Comment: If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam fil
by
Pierre Lindenbaum
154k
1) read groups should have been specified from the start (eg. with bwa mem -R ) 2) if you do'nt specify SORT_ORDER, the order is the same …
Comment: Asking for feedback on a Python library for computing alignments
by
Alexander
▴ 100
Does it support substitution matrices - e.g. blossum62 - for local protein alignments ? Does it support different gaps for gat open, and …
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