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0 votes
1 reply
658 views
Empty .best and .sing2 Files After Running Demuxlet
biosciences demuxlet
updated by Ram Ram • written by eking28 • eking28
0 votes
5 replies
1.9K views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
rna-seq featurecounts hisat
updated by Ram Ram • written by Prawesh • Prawesh
1 vote
3 replies
2.8K views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
pe bam sam flag paired-end
written by kalavattam • kalavattam
0 votes
2 replies
2.2K views
How to interpret infinite odds ratio?
statistics
written by Lukas • Lukas
0 votes
2 replies
1.2K views
Duplicated sequence samtools
bowtie2 samtools
updated by GenoMax GenoMax • written by Moinuddin • Moinuddin
0 votes
0 replies
481 views
reference-free assembly error assessment tools
assembly
written by lagartija lagartija
0 votes
4 replies
1.7K views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq vcf variant-calling
written by Esraa • Esraa
2 votes
0 replies
26K views
Herald: The Biostar Herald for Monday, May 13, 2024
herald
written by Biostar Biostar
0 votes
1 reply
1.5K views
Splitting Seurat object by sample layers
seurat
updated by Ram Ram • written by kilcdincer • kilcdincer
0 votes
5 replies
2.0K views
Galaxy StringTie error
stringtie galaxy
updated by Ketan • Ketan • written by trkfs • trkfs
0 votes
0 replies
674 views
dbNSFP sift scores integration
sift vep dbnsfp
written by atariw • atariw
0 votes
1 reply
1.1K views
Mouse ribosome sequences in fasta format
fasta mm10 rrna
updated by GenoMax GenoMax • written by octpus616 • octpus616
0 votes
4 replies
1.8K views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus annotation assembly genome
updated by Juke34 Juke34 • written by Vijith • Vijith
0 votes
1 reply
752 views
consensus sequence calling
consensus
updated by bk11 • bk11 • written by G.S • G.S
0 votes
3 replies
1.0K views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
seurat single-cell scrna-seq r
updated by Ram Ram • written by yau • yau
0 votes
2 replies
1.4K views
imputation through beagle
panel beagle reference imputation
written by Bushra Bibi Bushra Bibi
0 votes
0 replies
653 views
Empty kernel in SEACells model
single-cell scanpy seacells python anndata
written by AlexStar • AlexStar
0 votes
1 reply
1.2K views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair samtools alignment
updated by aw7 • aw7 • written by Zeng Hao • Zeng Hao
0 votes
0 replies
623 views
Reference panel of normals for ensembl named refgenome
mutect2
written by gernophil • gernophil
1 vote
0 replies
608 views
Producing sequence for splicing isoforms
isoform rmats splicing alternative spladder
written by tomas4482 • tomas4482
0 votes
6 replies
2.5K views
BWA alignment
samtools bam
updated by a.alnawfal.1992 a.alnawfal.1992 • written by Vahid • Vahid
0 votes
2 replies
1.5K views
Publish a Letter in higher impact vs Research article in lower impact
article letter journal
updated by ATpoint ATpoint • written by jennyp0706 • jennyp0706
0 votes
1 reply
1.1K views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence university assembly protein genomics
updated by Philipp Bayer Philipp Bayer • written by samRayne • samRayne
0 votes
1 reply
916 views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
mendelian-randomization
updated by Ram Ram • written by Nikki • Nikki
0 votes
14 replies
5.6K views
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated by Anitha • Anitha • written by ww22runner • ww22runner
0 votes
1 reply
965 views
Generating .bed file and .map file for polyploid vcf file through plink
bed polyploid map plink
updated by chrchang523 chrchang523 • written by Bushra Bibi Bushra Bibi
0 votes
0 replies
562 views
lncRNA
tcga lncrna
written by jain72744 • jain72744
0 votes
1 reply
788 views
Nomalization - TCGA, RNA-seq and Microarray
tcga rna-seq nomalization microarray
updated by Zhenyu Zhang Zhenyu Zhang • written by jain72744 • jain72744
0 votes
5 replies
2.3K views
Tissue-specific DEG analysis with DEseq2
deseq2 rna-seq deg r
updated by arctic • arctic • written by M. • M.
0 votes
2 replies
1.8K views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
combat-seq limma rna-seq removebatcheffect batch-effect
updated by Ram Ram • written by t.fortunato.asquini • t.fortunato.asquini
0 votes
2 replies
887 views
Output file of samtools flagstat empty
samtools-flagstat
updated by colindaven colindaven • written by ramendra.sarma • ramendra.sarma
0 votes
8 replies
2.6K views
joint callset and vcf sorting, unknown TAG issue
sort bcftools glnexus merge vcf
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Matteo Ungaro • Matteo Ungaro
0 votes
0 replies
668 views
News: Online course: An Introduction to Nanopore Direct RNA Sequencing
nanopore rnaseq
written by Physalia-courses Physalia-courses
1 vote
1 reply
2.0K views
input file in rmats
rmats
updated by Mathew • Mathew • written by Lambodarswain316 • Lambodarswain316
0 votes
3 replies
15K views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated by Mathew • Mathew • written by Christopher • Christopher
0 votes
7 replies
2.7K views
Longest transcript variant per gene
transcript longest variant orthofinder
written by san96 • san96
0 votes
3 replies
2.2K views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio cibersort r
written by Azra • Azra
0 votes
1 reply
924 views
Failed to open VCF file
gatk sentieon bwa-mem
updated by Pierre Lindenbaum Pierre Lindenbaum • written by melissachua90 • melissachua90
2 votes
7 replies
9.4K views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated by RT • RT • written by xiaozhongzhiping • xiaozhongzhiping
0 votes
4 replies
1.7K views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
written by beginner123 • beginner123
3 votes
6 replies
16K views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic paired-end
updated by Carlo Yague Carlo Yague • written by dllopezr • dllopezr
0 votes
2 replies
981 views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated java.nio.bufferunderflowexception haplotypecaller bqsr
written by Bushra Bibi Bushra Bibi
0 votes
11 replies
2.5K views
In IGV is this a heterogeneous mutation or false call?
mutations igv heterogeneous
written by Tuck898 • Tuck898
0 votes
3 replies
1.1K views
what is another word for a BLAST "hit"?
blast alignment
written by dec986 dec986
0 votes
1 reply
561 views
extract viral protein of interest from 10k whole viral genomes
nblast viral-genome
updated by Ram Ram • written by Shwetha • Shwetha
0 votes
0 replies
615 views
Marker Features variance by cluster, sample, and treatment group
seurat scatac-seq archr
updated by Ram Ram • written by naomiboldon • naomiboldon
0 votes
3 replies
1.5K views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk vcf liftover
updated by Ram Ram • written by Omics data mining Omics data mining
2 votes
6 replies
14K views
samtools tview symbols
samtools
updated by Ashutosh Pandey Ashutosh Pandey • written by biolab biolab
0 votes
9 replies
2.6K views
Filtering Multi-sample VCF file for all except one Genotype
variant snp vcf
updated by Pierre Lindenbaum Pierre Lindenbaum • written by schmince • schmince
0 votes
5 replies
1.5K views
Too many unpaired forward reads found by Trimmomatic
trimmomatic
written by SilhouetteQ • SilhouetteQ
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