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159 results • Page
2 of 4
Sort: replies
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Views
Votes
Replies
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
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
2
replies
774
views
Error in mvnX when running processSamples.R of OncoCNV
variant-calling
oncocnv
cnv
updated 2 days ago by
Ram
39k • written 3.5 years ago by
mwarrier
• 0
0
votes
2
replies
952
views
error while executing panX script (KeyError: 'db_xref').
linux
python
genome
biopython
updated 1 day ago by
Ram
39k • written 2.8 years ago by
Kumar
▴ 100
0
votes
2
replies
187
views
What does "OS_CNSR" and "PFS_CNSR" mean?
survival
cancer
r
1 day ago by
JACKY
▴ 100
0
votes
2
replies
134
views
If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam file, do I have to re-sort and re-mark duplicates?
read
groups
bam
addorreplacereadgroups
4 hours ago by
javiflaja
• 0
0
votes
2
replies
133
views
Blast reads classification
NGS
magicblast
blast
updated 12 hours ago by
Ram
39k • written 16 hours ago by
Giulia.cosenza
▴ 80
0
votes
2
replies
224
views
Correct way to remove Nextera adapters from ITS sequences
adapters
ITS
trimmomatic
2 days ago by
mattze731
▴ 10
0
votes
2
replies
1.4k
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
2
replies
1.7k
views
How to handle NaN in emmax Kinship matrix?
GWAS
SNP
updated 1 day ago by
Thu
• 0 • written 5.1 years ago by
CWesse
• 0
0
votes
2
replies
357
views
BedGraph to bigWig
bigWig
BedGraph
Galaxy
ATAC-seq
updated 1 day ago by
Ram
39k • written 5 months ago by
abhay.kanodia
▴ 10
1
vote
2
replies
211
views
Combination of ROC CURVE
roccurve
R
AUC
4 days ago by
Maria17
▴ 20
0
votes
2
replies
109
views
Chain file for Homo_sapiens_assembly38.fasta to liftover Nebula vcf
hg38
fasta
hg19
chainfile
17 hours ago by
berndmann
▴ 10
1
vote
2
replies
207
views
phage genome submission in ncbi genebank
phage
table2asn
ncbi
1 day ago by
tahsinkhan570
• 0
0
votes
2
replies
250
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
3 days ago by
demoraesdiogo2017
▴ 90
0
votes
2
replies
199
views
Samtools index and sambamba-depth error?
linux
samtools
indexing
sambamba
updated 18 hours ago by
jkbonfield
★ 1.0k • written 15 days ago by
MobiusT
▴ 10
1
vote
2
replies
524
views
How to mine plant-inducible promoter (PIP) box from Xanthomonas genus genome?
assembly
gene
genome
next-gen
updated 3 days ago by
Ram
39k • written 3.6 years ago by
Kumar
▴ 100
3
votes
2
replies
883
views
Creating a genotype matrix for BeviMed
snp
genome
Bayesian
updated 1 day ago by
Ram
39k • written 3.4 years ago by
tacrolimus
▴ 110
0
votes
1
reply
904
views
Strange output from Homer findPeaks
homer
atac-seq
updated 1 day ago by
Ram
39k • written 3.5 years ago by
fr
▴ 200
0
votes
1
reply
935
views
ATAC seq enhancer help
alignment
ATAC-seq
bowtie2
DNA
Enhancers
updated 1 day ago by
Ram
39k • written 3.7 years ago by
mrs.whirly
• 0
0
votes
1
reply
71
views
GSEA application not launching
GSEA
updated 8 hours ago by
GenoMax
130k • written 8 hours ago by
Jen
▴ 40
0
votes
1
reply
142
views
Is the Kruskal-Wallis test appropriate for genomic distances?
Statistics
updated 1 day ago by
Ram
39k • written 1 day ago by
aaronlogsdon2001
• 0
1
vote
1
reply
116
views
snps from empty well, Illumina Sequencing
Illumina
SNP
sequencing
updated 1 day ago by
GenoMax
130k • written 1 day ago by
saint-even
• 0
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
1
reply
131
views
UCSC genome browser
Genome-browser
shannon-entropy
updated 13 hours ago by
Ram
39k • written 1 day ago by
Lkhagvadulam
• 0
0
votes
1
reply
757
views
differential expression of geodataset using limma (input files)
R
gene
updated 1 day ago by
Ram
39k • written 3.4 years ago by
firstorthopedicdoctor
▴ 30
0
votes
1
reply
126
views
How to add annotation columns with specific colors to the heatmap?
R
heatmap
RNA-seq
updated 13 hours ago by
Ram
39k • written 1 day ago by
ahmad mousavi
▴ 750
0
votes
1
reply
386
views
How to quantification proteomics data
proteomics
updated 3 days ago by
eqoa45
• 0 • written 19 months ago by
LeeLee
▴ 10
1
vote
1
reply
1.4k
views
How to analyze DNA data with UMI
next-gen-sequencing
umi
updated 1 day ago by
Ram
39k • written 3.2 years ago by
deniselavezzari
• 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
1
reply
132
views
CIBERSORT Error: File not found
CIBERSORT
updated 1 day ago by
ATpoint
72k • written 2 days ago by
jcara514
• 0
0
votes
1
reply
707
views
Is there bioinformatics tool to check cross hybridization between primers and probes?
primer
cross-hybridisation
pcr
updated 1 day ago by
Tawny
▴ 180 • written 2.7 years ago by
Pramod Shinde
• 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
1
reply
113
views
What is the possibility of Depth (DP) being higher than the coverage
GATK
DP
Coverage
Depth
HaplotypeCaller
updated 1 day ago by
seidel
11k • written 1 day ago by
dare_devil
★ 3.1k
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
1
reply
107
views
How to remove cloning vector sequence from bacterial assembled genome?
assembly
removal
bacterial
genome
vector
updated 15 hours ago by
GenoMax
130k • written 20 hours ago by
mathavanbioinfo
▴ 70
0
votes
1
reply
749
views
plasmid spades R1/R2 files?
plasmid
sequencing
updated 6 days ago by
Ram
39k • written 3.8 years ago by
sarah.goldstein
• 0
0
votes
1
reply
825
views
Error in MEGAHIT
Assembly
next-gen
metagenomic
updated 1 day ago by
Ram
39k • written 3.4 years ago by
nisrinalulu
▴ 10
0
votes
1
reply
867
views
deeptools plotHeatmap gives blurry pixelated image
computeMatrix
plotHeatmap
deeptools
ATAC-seq
updated 1 day ago by
Ram
39k • written 2.4 years ago by
Himanshu C
• 0
0
votes
1
reply
163
views
Error occured at the PHG imputation step: allele in genotype not in the variant context
PHG
Imputation
PracticalHaplotypeGraph
Haplotype
updated 14 hours ago by
lcj34
▴ 230 • written 3 days ago by
xeod21
• 0
0
votes
1
reply
136
views
DESeq2 for different design and normalized counts
DESeq2
log2foldchange
updated 1 day ago by
ATpoint
72k • written 1 day ago by
t.ru
▴ 20
0
votes
1
reply
114
views
Alternative To interactions comparison in limma in DESeq2
DESeq2
interactions
updated 1 day ago by
ATpoint
72k • written 1 day ago by
f2ff7a46
• 0
0
votes
1
reply
262
views
Comparing loci across catalogs
Stacks
reference
alignment
RADseq
adegenet
updated 6 days ago by
rycro_c
• 0 • written 13 months ago by
Austin
• 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
1
reply
108
views
Filtering genes after TPM normalization
filtering
normalization
TPM
r
updated 11 hours ago by
Meisam
▴ 190 • written 12 hours ago by
JACKY
▴ 100
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
1
vote
1
reply
105
views
Plotting GO enrichment DATA
R
GO
enrichment-analysis
updated 13 hours ago by
Ram
39k • written 21 hours ago by
hellokwmin
• 0
0
votes
1
reply
397
views
pal2nal -nogap -nomismatch options not working
pal2nal
updated 1 day ago by
Marie
• 0 • written 6 months ago by
pkfsantos
• 0
0
votes
1
reply
716
views
MMSplice score interpretation
mmsplice
splice-effect-prediction
updated 1 day ago by
Ram
39k • written 2.7 years ago by
Augusta
▴ 30
0
votes
1
reply
476
views
Msc in bioinformatics recommendation
career
updated 1 day ago by
Ram
39k • written 3.3 years ago by
fyfes
▴ 70
159 results • Page
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Recent Votes
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
Comment: ChatGPT optimized for bioinformatics questions
Answer: Reorder GO terms using R
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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
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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…
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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 …
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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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May be you can consider to make a talk about that work for your community "sciBerloga" - see previous talks: https://www.youtube.com/@SciBe…
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[**On this page**][1] Transcriptome: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/GRCh37_mapping/gencode.v43lift…
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If you have not, look in "System settings" and "security" to see if the OS is blocking the application from launching.
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I made changes to how I decode m6A events and updated links in the answer above. Python code is in a separate repository. Javascript code i…
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