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72 results • Page
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73
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
normalization
deseq2
host-pathogen
rna-seq
21 hours ago by
r-ninja
▴ 20
0
votes
0
replies
75
views
News:
UCSC Xena Webinar Series: Visualize and Analyze Bulk Sequencing Data on Xena
visualization
genomics
cancer
21 hours ago by
Mary Goldman
• 0
0
votes
6
replies
462
views
FraserDataSet() error in FRASER
R
splicing
FRASER
RNAseq
alternative
5 days ago by
n_navy
▴ 10
0
votes
0
replies
236
views
Job:
Postdoctoral Fellow in Machine Learning and Computational Biology, The University of Memphis
PTSD
learning
bioinformatics
deep
genomics
5 days ago by
bjdaigle
▴ 10
0
votes
2
replies
128
views
Download GenomicSEM reference file
GenomicSEM
updated 6 hours ago by
1769mkc
★ 1.3k • written 16 hours ago by
zhangmyharper
• 0
0
votes
0
replies
270
views
Job:
Head of Bioinformatics Facility (m/f/div) at Max Planck Institute of Epigenetics
germany
e14
6 days ago by
elsalatino
• 0
0
votes
1
reply
282
views
Reference-guided transcriptome assembly using multiple SRA experiments ?
assembly
Transcriptome
projects
SRA
updated 6 days ago by
lieven.sterck
15k • written 7 days ago by
debitboro
▴ 270
0
votes
1
reply
80
views
SSL and Syntax Errors when using fasterq-dump (SRA Toolkit)
sratoolkit
updated 4 hours ago by
GenoMax
151k • written 12 hours ago by
QURROTU AINI
• 0
0
votes
1
reply
72
views
Drastic drop in RNA-seq read mapping rate when disabling gaps in Bowtie2
bowtie2
updated 4 hours ago by
GenoMax
151k • written 6 hours ago by
triplee0305
▴ 10
0
votes
1
reply
81
views
European Variation Archive submission eva-sub-cli validation failure: "Sample name concordance check"
eva-sub-cli
EuropeanVariationArchive
submission
database
3 hours ago by
askhat
• 0
0
votes
4
replies
355
views
error in reading codelink data
readcodelinkset
6 days ago by
nazaninhoseinkhan
▴ 530
0
votes
0
replies
321
views
mtDNA variants from WGS data
mitogenome
WGS
updated 6 days ago by
Ram
45k • written 7 days ago by
wonde2000
• 0
0
votes
1
reply
346
views
Phylogeny aware alignment input
HoSeq
MSA
updated 2 hours ago by
zjq6666666
• 0 • written 11 months ago by
Meto
• 0
0
votes
0
replies
1
view
RNA-seq analysis
STAR
HiSat2
featurecounts
just now by
SEJAL
• 0
0
votes
0
replies
614
views
Job:
Postdoc fellow - genetics, proteomics, single cell and bioinformatics, Indiana University, Indianapolis, USA
single-cell
bioinformatics
proteomics
genetics
updated 6 days ago by
Ram
45k • written 19 days ago by
Jingwen
• 0
0
votes
2
replies
1.6k
views
Analysing Problem Seen In MEGA X
Alignment
MEGAX
Muscle
updated 3 days ago by
humarafique.1234
• 0 • written 3.6 years ago by
ankurhalder116
• 0
0
votes
1
reply
177
views
Perturb seq
perturbseq
updated 2 days ago by
GenoMax
151k • written 2 days ago by
shlo12
• 0
0
votes
0
replies
217
views
discrepancies in ORA results between g:Profiler (gost) and clusterProfiler (enrichGO)
Analysis
Enrichment
written 3 days ago by
ricardo
• 0
0
votes
0
replies
222
views
Job:
Two postdoctoral positions in generative AI and blood-based cancer detection, Aarhus University, Denmark
nucleosomes
post_doc
cancer_detection
generativeAI
bioinformatics
1 day ago by
Jakob Skou
• 0
0
votes
0
replies
107
views
q-value threshold for omics data when performing univariate cox analysis
MachineLearning
q-value
Cox
FDR
omics
1 day ago by
Yugan Gogul Muthukumar
▴ 10
0
votes
1
reply
331
views
News:
9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4, 2025) -- SUMMER IN BERLIN --
Workshop
RNA-Seq
transcriptomics
VariantCalling
DNA-Seq
1 day ago by
ecSeq Bioinformatics
▴ 20
0
votes
3
replies
525
views
Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Acinetobacter guillouiae
nif
NCBI_genome_database
Acinetobacter_guillouiae
Nitrogenase
Nitrogen_fixation
updated 4 days ago by
GenoMax
151k • written 4 days ago by
Nafi
• 0
72 results • Page
2 of 2
Recent Votes
C: How to convert extended CIGAR to regular CIGAR
Answer: Trim CDS to ORF
Comment: How common is it to split fastq files prior to bwa mem to increase parallelizati
Answer: Obtaining Q30/Q60 Values from Fastq Files
Answer: What are the advantages of using the T2T as a reference vs GRCh38 today?
Comment: Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
Answer: DESeq2 outliers-should I be concerned?
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Popular Question
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joe_genome
▴ 50
Scholar
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ATpoint
88k
Popular Question
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graeme.thorn
▴ 110
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erikatatianacs
• 0
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ltalignani
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dsull
★ 7.5k
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triplee0305
▴ 10
Recent Replies
Comment: The allele with index 2 is not defined in the REF/ALT columns" error after AF fi
by
erikatatianacs
• 0
yes, but I think that I need it in this way because the main idea if filter by the population AF, so I dont need the AF of the sample
Comment: Trim CDS to ORF
by
jaredbernard
▴ 30
Thanks, @lievensterck. I'll look into those to see if they can accommodate the designated offset.
Comment: The allele with index 2 is not defined in the REF/ALT columns" error after AF fi
by
Pierre Lindenbaum
166k
by the way, when using bcftools annotate this way, you would overwrite the original AF field with the value of gnomad. https://samtools.…
Answer: Trim CDS to ORF
by
lieven.sterck
15k
Why not use an ORF finder tool? eg. getORF , longestORF, transdecoder, FrameD, ... many options. Unless yo have prior knowledge on your…
Comment: Trim CDS to ORF
by
Pierre Lindenbaum
166k
give us a full example please (fasta...)
Comment: The allele with index 2 is not defined in the REF/ALT columns" error after AF fi
by
Pierre Lindenbaum
166k
there was already a problem before bcftools nom . Do you still have two alleles in sample_raw.vcf.gz at the same position ? if true you s…
Answer: Mageck RRA is listing negative controls as high fold change in the gene summary
by
ltalignani
• 0
I'm having the same problem: in my `gene_summary.txt`, these negative controls appear. I used the following script: #!/bin/bas…
Comment: Obtaining Q30/Q60 Values from Fastq Files
by
joe_genome
▴ 50
thanks that makes sense! thanks for sharing the link!
Comment: Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
by
Bastien Hervé
6.3k
Thanks for the troubleshooting ! > Seurat::RunPCA forces the usage of the scale.data layer. And it disables centering (center = NULL) The…
Comment: RNASeq bulk transcriptomics analysis
by
lieven.sterck
15k
just out of curiosity, and for completeness, can you provide the numbers that you used to get to the 'only 37% mapped' result?
Comment: RNASeq bulk transcriptomics analysis
by
lieven.sterck
15k
Hopefully, because there aren't any other explanations :)
Comment: The allele with index 2 is not defined in the REF/ALT columns" error after AF fi
by
erikatatianacs
• 0
I am using bcftools 1.19 Using htslib 1.19 the ouput > chr1 114940632 . C CA 115.328 PASS INDEL;IDV=32;IMF=0.820513;DP=39;VDB=0.108342;S…
Comment: The allele with index 2 is not defined in the REF/ALT columns" error after AF fi
by
Pierre Lindenbaum
166k
that would be a problem with `bcftools norm`. What is your version of bcftools ? Furthermore, show us the output of bcftools view -G -…
Comment: RNASeq bulk transcriptomics analysis
by
rajdeepboral00
▴ 60
1)I have checked for rRNA, but no such contamination was found. 2) & 3) Yes that could be the possibility though. Thanks.
Comment: How common is it to split fastq files prior to bwa mem to increase parallelizati
by
ATpoint
88k
I cannot tell about "industry-standard", but since it was developed in coop. with the bwa developer, and claims that it produces identical …
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