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0 votes
0 replies
712 views
How to annotate a bed file using gtf using python
gtf bed
updated by Ram Ram • written by naveedhasan2000 • naveedhasan2000
0 votes
2 replies
1.5K views
trying to do some GSEA in python
python gsea go
updated by Wayne Wayne • written by aleksk779 • aleksk779
0 votes
0 replies
834 views
Issues while trying to create my own PON (Panel Of Normals) with GATK
vcf gatk somatic genomics variants
written by Samuel • Samuel
0 votes
2 replies
2.4K views
ENCODE Hi-C FASTQ files are SINGLE end
fastq layout encode hi-c
updated by Yihang • Yihang • written by hamarillo • hamarillo
0 votes
1 reply
922 views
Seeking Proper Interpretation of Dispersion Graph: A Call for Statistical and Biological Insight
rnaseq deseq2 dispersionplot
updated by ATpoint ATpoint • written by Pumla • Pumla
0 votes
3 replies
1.4K views
cell type adjustment - how many cell types to include?
celltypes ewas
updated by LChart LChart • written by kaybelter • kaybelter
0 votes
0 replies
930 views
OrthoVenn3 Singletons
venn singletons orthovenn orthofinder
updated by GenoMax GenoMax • written by Lasya • Lasya
0 votes
1 reply
806 views
AUC=1, is it possible after lasso regression?
lasso auc
updated by Jeremy Leipzig Jeremy Leipzig • written by Amir • Amir
0 votes
0 replies
785 views
Dante Labs VCF analysis, CHROM column absence UPD: solved!
vcf coordinate dante assembly chromosome
written by k.alincha k.alincha
0 votes
5 replies
1.8K views
How to assure that sequence consensus is genuine?
genome
written by marongiu.luigi marongiu.luigi
0 votes
4 replies
1.6K views
How evaluate assembly when multiple reference strains are available?
genome quast reference assembly
updated by dthorbur dthorbur • written by MetaPaul • MetaPaul
0 votes
1 reply
855 views
Need help with improving the 16S rRNA sequence quality with trimmomatic?
bioinformatic trimmomatic
updated by jeevii • jeevii • written by Kai Xin • Kai Xin
1 vote
1 reply
759 views
Forgot the web site with comparison of NGS platforms
ngs platforms
updated by cmdcolin cmdcolin • written by konstantinkul konstantinkul
0 votes
1 reply
957 views
How to keep only first part of the name when adding AddOrReplaceReadGroups in multiple BAM files at a time?
slurm bash gatk picard
written by kabir.deb • kabir.deb
0 votes
7 replies
2.0K views
Help with summarizeOverlaps function in RNASeq analysis using R
r rna-seq summarizeoverlaps genomicalignments
updated by BioinfGuru BioinfGuru • written by FJCF • FJCF
0 votes
1 reply
1.5K views
Data table for LOEUF loss-of-function observed/expected upper bound fraction
loeuf
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Shicheng Guo Shicheng Guo
0 votes
2 replies
1.3K views
Why are gene models from JGI non-sense when using AGAT to to extract proteins?
translation models gif gene cgi
written by O.rka O.rka
0 votes
0 replies
916 views
details about PCA in plink 2.0: eigenvectors, PCs, scores
gwas plink pca
written by kaybelter • kaybelter
0 votes
2 replies
984 views
Database for non cancer cell lines
cell-line l1000 rna-seq cancer-database lincs
written by ANSARAHMAD • ANSARAHMAD
0 votes
2 replies
1.2K views
Convert to ENTREZGENE
maize entrez
written by san96 • san96
0 votes
1 reply
1.4K views
How to calculate depth of coverage and applying read depth filter
depth-of-coverage cram wgs
updated by Ram Ram • written by Sd • Sd
0 votes
3 replies
1.9K views
BioGRID REST - How to retrieve all the protein interactions?
biogrid python rest
updated by Pierre Lindenbaum Pierre Lindenbaum • written by dbykov • dbykov
0 votes
4 replies
1.5K views
Problem generating paired end reads when converting Cell Ranger's BAM result to FASTQ
fastq bam
written by ntuzov • ntuzov
0 votes
1 reply
830 views
Finding chimeric reads for CRISPR edited mouse cells from RNA-Seq data
rna-seq crispr
updated by Haci Haci • written by Ethan • Ethan
1 vote
7 replies
2.2K views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
jbrowse jbrowse2
updated by cmdcolin cmdcolin • written by I0110 I0110
0 votes
1 reply
1.1K views
Tissue specific mRNA expression dataset in human and mouse
tissue-specificity
updated by Ram Ram • written by Shicheng Guo Shicheng Guo
0 votes
3 replies
4.1K views
Mapping ortholog human and mouse transcript
biomart
written by 1769mkc 1769mkc
0 votes
3 replies
1.1K views
How do I get the gene annotations as a text file from a genbank file?
sequence-annotation genbank
updated by Ram Ram • written by eae6d2e7 • eae6d2e7
1 vote
2 replies
1.7K views
News: Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Volume II
mathematical-modelling endocrinology ml systems-biology machine-learning
written by Johannes W. Dietrich • Johannes W. Dietrich
0 votes
1 reply
747 views
Alignment with new reference
alignment
updated by GenoMax GenoMax • written by marco.barr • marco.barr
0 votes
1 reply
927 views
Bowtie2 alignment rate
galaxy bowtie alignment-rate
updated by jeevii • jeevii • written by pavithraashokkumar818 • pavithraashokkumar818
0 votes
1 reply
888 views
Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
scrna rnaseq
updated by Soheil • Soheil • written by sithlordashley • sithlordashley
1 vote
0 replies
734 views
Synthetic lethality and cancer database
interaction lethal synthetic
written by Shicheng Guo Shicheng Guo
0 votes
9 replies
3.6K views
Error in openning FastQC
fastqc igv
updated by GenoMax GenoMax • written by huynhthienphai • huynhthienphai
0 votes
2 replies
1.6K views
vcf file: number of samples does not match number of columns
vcf bcftools
written by ekirsch • ekirsch
0 votes
4 replies
1.2K views
Is it reasonable to discard reads that show variation of quality across its length?
trimming
written by BRENO • BRENO
0 votes
5 replies
1.7K views
Error running local blastn in R using system2
blastn ncbi r
written by Harrison • Harrison
3 votes
10 replies
3.0K views
Forum: F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated by Madelaine Gogol Madelaine Gogol • written by Ann Ann
0 votes
0 replies
667 views
News: Online course: Reproducibility in Bioinformatics
singularity version-control docker containers
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
0 replies
502 views
News: Online course: Analysis of Prokaryotic Pangenomes (Last call)
prokaryotic bacterial-genomics pangenomics
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
1 reply
884 views
Annotation of Complex genomes using NCBI Genome Workbench
genome-workbench maker
updated by Lissa Cruz Saavedra • Lissa Cruz Saavedra • written by SAsciences • SAsciences
0 votes
1 reply
918 views
Looking for RPIP Illumina kit probe sequences
sequences illumina
updated by GenoMax GenoMax • written by David Tachiquín • David Tachiquín
0 votes
9 replies
2.1K views
Low number of both surviving reads after trimming
trimmomatic trimming
written by Jay • Jay
0 votes
2 replies
982 views
ONT direct RNA sequencing
drs ont
updated by Ram Ram • written by Karina • Karina
0 votes
4 replies
1.2K views
Number of CPUs to use by DRAP for transcriptomic assmbly
drap cpu transcriptomics
written by Mohamed Abderrahmane • Mohamed Abderrahmane
0 votes
2 replies
1.2K views
Gene reads all zero for each sample
r salmon de deseq2
written by DYLAN NICO • DYLAN NICO
0 votes
2 replies
1.1K views
Can I have multiple active GDC download tokens?
tcga
updated by Zhenyu Zhang Zhenyu Zhang • written by mrk • mrk
1 vote
0 replies
635 views
Contradictions in GSEA results
gsea enrichment-analysis pea
updated by Ram Ram • written by Tolga • Tolga
0 votes
0 replies
595 views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation transposons phagetermini sequencing
written by alenew.am • alenew.am
0 votes
3 replies
3.7K views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
findallmarkers seurat re-clustering
written by Nitin • Nitin
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