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72 results • Page 2 of 2
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73
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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
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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
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FraserDataSet() error in FRASER
R splicing FRASER RNAseq alternative
5 days ago by n_navy ▴ 10
0
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0
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236
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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
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Download GenomicSEM reference file
GenomicSEM
updated 6 hours ago by ★ 1.3k • written 16 hours ago by • 0
0
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0
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270
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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
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Reference-guided transcriptome assembly using multiple SRA experiments ?
assembly Transcriptome projects SRA
updated 6 days ago by 15k • written 7 days ago by ▴ 270
0
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1
reply
80
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SSL and Syntax Errors when using fasterq-dump (SRA Toolkit)
sratoolkit
updated 4 hours ago by 151k • written 12 hours ago by • 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 151k • written 6 hours ago by ▴ 10
0
votes
1
reply
81
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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
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355
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error in reading codelink data
readcodelinkset
6 days ago by nazaninhoseinkhan ▴ 530
0
votes
0
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321
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mtDNA variants from WGS data
mitogenome WGS
updated 6 days ago by 45k • written 7 days ago by • 0
0
votes
1
reply
346
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Phylogeny aware alignment input
HoSeq MSA
updated 2 hours ago by • 0 • written 11 months ago by • 0
0
votes
0
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1
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RNA-seq analysis
STAR HiSat2 featurecounts
just now by SEJAL • 0
0
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0
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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 45k • written 19 days ago by • 0
0
votes
2
replies
1.6k
views
Analysing Problem Seen In MEGA X
Alignment MEGAX Muscle
updated 3 days ago by • 0 • written 3.6 years ago by • 0
0
votes
1
reply
177
views
Perturb seq
perturbseq
updated 2 days ago by 151k • written 2 days ago by • 0
0
votes
0
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217
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discrepancies in ORA results between g:Profiler (gost) and clusterProfiler (enrichGO)
Analysis Enrichment
written 3 days ago by • 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
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107
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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
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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 151k • written 4 days ago by • 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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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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