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Showing top results for tag: RSEM • reset
5
votes
3
replies
660
views
Why Are Transcripts Differentially Expressed but Not Genes in RNA-seq Analysis? — Confusion Around Transcript-Level Differential Expression
Gene Transcript Count RSEM
9 days ago by Cooper • 0
0
votes
15
replies
936
views
I have encountered some bugs in transcriptome analysis using STAR and RSEM.
STAR RSEM
updated 4 weeks ago by 55k • written 4 weeks ago by • 0
0
votes
0
replies
155
views
Using RSEM after Cuffcompare
RNA-seq cuffcompare RSEM
9 weeks ago by ZZOYEA ▴ 20
0
votes
1
reply
345
views
Fragment size of published single end RNAseq data
NGS single-end RNA-seq RSEM
updated 3 months ago by 44k • written 3 months ago by • 0
3
votes
4
replies
667
views
RSEM getting TPM from STAR alignment
TPM STAR RNAseq RSEM
4 months ago by Emily ▴ 20
2
votes
2
replies
902
views
Salmon vs Kallisto vs RSEM
RSEM quantification kallisto Salmon
5 months ago by Mohamed Abderrahmane ▴ 20
4
votes
7
replies
905
views
To get p-values for the TPM
P-value TPM RSEM
updated 6 months ago by ★ 6.9k • written 6 months ago by • 0
0
votes
1
reply
581
views
Is it possible to use RSEM with BAM files from STAR alignment?
RSEM alignment Pre-computed STAR
updated 6 months ago by ▴ 340 • written 2.4 years ago by • 0
7
votes
15
replies
1.6k
views
6 follow
I would like to exclude rRNA in RSEM and quantify other genes.
STAR RNA-seq RSEM
updated 9 months ago by ★ 6.9k • written 9 months ago by ▴ 170
0
votes
3
replies
1.0k
views
Empty genes.bam files in RSEM-STAR workflow
star rsem
updated 10 months ago by 101k • written 20 months ago by ▴ 30
0
votes
4
replies
951
views
using RSEM with non Trinity assembly
SPAdes Trinity RSEM
updated 11 months ago by ★ 2.7k • written 11 months ago by ▴ 10
2
votes
4
replies
926
views
An issue with gtf file (ballgownrsem)
Ballgown RNA-seq GTF RSEM
11 months ago by cucindarko51 • 0
0
votes
0
replies
307
views
Low mapping after Cufflinks assembly
assembly gffread cuffmerge Cufflinks RSEM
11 months ago by sofiablancoglez • 0
0
votes
0
replies
316
views
coupling Cufflinks results with RSEM
transcript-level-quantification RSEM transcriptome-assembly Cufflinks
11 months ago by sofiablancoglez • 0
0
votes
0
replies
371
views
Issues while running abundance_estimates_to_matrix.pl
RSEM Denovo RNA-seq abundance-estimate
12 months ago by Foad ▴ 10
2
votes
4
replies
2.5k
views
Information on "sample_name.cnt" obtained by an RSEM analysis
RNA-Seq RSEM
updated 12 months ago by 44k • written 4.2 years ago by • 0
0
votes
2
replies
1.3k
views
RSEM not giving .genes.results and isoforms.results ; Plase check if you provide correct parameters/options for the pipeline!
genomics transcriptome rsem ngs
13 months ago by kat.bi • 0
0
votes
1
reply
633
views
Convert RNASeq V2 data in cBioPortal having RSEM normalized results to TPM values
TPM RNA-Seq cbioportal RSEM
updated 12 months ago by 44k • written 13 months ago by • 0
0
votes
1
reply
665
views
What gene annotation was used for PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset?
RNAseq RSEM TCGA
updated 13 months ago by ★ 1.2k • written 13 months ago by • 0
5
votes
3
replies
1.3k
views
RSEM uses different gene lengths for each sample.
STAR RNA-seq RSEM
15 months ago by Apprentice ▴ 170
0
votes
5
replies
1.1k
views
Solution for pop-up problem with rsem-prepare-reference (RSEM can not recognize reference sequence name ATM...)
rsem
15 months ago by tsogurlu • 0
0
votes
1
reply
598
views
Pre-filtering of annotated isoforms based on splice junctions
RSEM isoforms splicing RNA-seq Kallisto
updated 16 months ago by ★ 2.5k • written 16 months ago by ▴ 160
4
votes
14
replies
2.7k
views
RSEM implementation
RSEM
updated 16 months ago by 44k • written 16 months ago by ▴ 140
0
votes
2
replies
992
views
Genecount-difference between HT-seq count, RSEM, and Kallisto
Kallisto RSEM RNAseq HTseqcount TPM
18 months ago by tvibhaps ▴ 10
0
votes
1
reply
784
views
Issue running RSEM
RSEM RNA
updated 18 months ago by 14k • written 18 months ago by ▴ 10
3
votes
3
replies
1.7k
views
Read counting in RSEM and Salmon (alignment mode)
quantification RSEM RNA-seq Salmon
18 months ago by predeus ★ 2.0k
0
votes
1
reply
498
views
RSEM expression values
RSem Trinity
updated 19 months ago by 44k • written 19 months ago by • 0
3
votes
4
replies
1.3k
views
RSEM calculate-expression has only one sample in .isoforms.results file
RSEM RNA-seq STAR
20 months ago by Daniel ▴ 30
2
votes
4
replies
1.6k
views
Unable to run RSEM because of error rsem-parse-alignments : No such file or directory
RNA-Seq Bowtie2 RSEM Boost
22 months ago by mohammedtoufiq91 ▴ 260
0
votes
1
reply
961
views
Consistency in the GTF files used for the index building of STAR alignment and RSEM
RSEM STAR alignment rna-seq gtf
updated 22 months ago by 44k • written 22 months ago by • 0
3
votes
5
replies
1.6k
views
Identify and remove contaminations in RNA-Seq dataset
rsem fastqc quantification alignment fastp
22 months ago by Abdul ▴ 10
0
votes
2
replies
1.1k
views
Good practices for RNA-seq (2x50, 2x75, 2x100) aligment with STAR + RSEM
RSEM RNA-seq STAR
updated 23 months ago by 14k • written 23 months ago by • 0
2
votes
6
replies
5.5k
views
6 follow
rsem prepare-reference error
rsem
updated 23 months ago by ▴ 10 • written 6.0 years ago by • 0
0
votes
0
replies
566
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
deseq2 rsem toil
2.0 years ago by Bioinformatician • 0
1
vote
4
replies
2.2k
views
How to use RSEM to quantify genes and transcript expression from STAR outpute file (Aligned.toTranscriptome.out.bam)
RSEM STAR
updated 2.2 years ago by 44k • written 2.2 years ago by ▴ 30
0
votes
0
replies
470
views
RSEM/edgeR/Trinity: Unsorted raw matrix produce nonsense rpkm() results?
RSEM edgeR Trinity
2.2 years ago by bioinfo2345 ▴ 40
3
votes
2
replies
1.4k
views
Does RSEM ignore STAR's splice-aware nature?
RSEM STAR
updated 2.3 years ago by 6.9k • written 2.3 years ago by ▴ 40
0
votes
0
replies
443
views
Invalid number of arguments rsem-calculate-expression
rsem bowtie
2.3 years ago by Patricia • 0
2
votes
1
reply
794
views
Good statistics for RNA-seq alignments using RSEM
cnt rsem stat rsem-calculate-expression alignment
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by • 0
0
votes
7
replies
1.8k
views
RSEM error
mapping transcriptomics RSEM genome alignment
2.4 years ago by glady ▴ 320
0
votes
0
replies
561
views
Doubt with Hisat2-RSEM counting
RSEM Hisat2 RNA-seq
2.4 years ago by JGMC • 0
4
votes
2
replies
774
views
Is there any way to normalize a sample with high number of reads assigned to it?
fastp sequencing depth RSEM STAR
updated 2.4 years ago by 21k • written 2.4 years ago by ▴ 70
0
votes
0
replies
680
views
Error on rsem-calculate-expression
RSEM
2.4 years ago by billyconan6a • 0
0
votes
2
replies
1.3k
views
RSEM prepare reference error
RSEM
2.4 years ago by billyconan6a • 0
3
votes
8
replies
2.3k
views
Survival or Correlation analysis based on Xena UCSC RSEM FPKM/TPM
TPM Xena RSEM FPKM rna-seq
2.4 years ago by Yang Shi • 0
0
votes
3
replies
841
views
Finding DEGs using script available in Trinity for RSEM
run_DE_analysis.pl Trinity RSEM DEGs
2.5 years ago by Roy.anupama11 • 0
0
votes
3
replies
750
views
Using RSem of Trinity, align_and_estimate_abundance.pl script, all folders for sample/condition is not being created
RSem Quantification Trinity
updated 19 months ago by 44k • written 2.5 years ago by • 0
0
votes
3
replies
784
views
RSEM Prepare Reference - transcriptome instead of genome reference?
RSEM RNA-seq
updated 23 months ago by 44k • written 2.5 years ago by ▴ 20
0
votes
6
replies
1.2k
views
Finding DEGs from HISAT2/STRINGTIE output
EdgeR pipeline BowTie Kallisto RSem DEGs
2.5 years ago by Roy.anupama11 • 0
1
vote
5
replies
1.3k
views
Use RSEM and Bowtie2 to align paired-end sequences
bowtie2 rsem
updated 2.6 years ago by 85k • written 2.6 years ago by ▴ 70
50 results • Page 1 of 1
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Explanation of DESeq factor leveling
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filterx : fast and efficient filter tool written in Rust for csv,fasta,fastq,gff,vcf,sam files.
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> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
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The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
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What p-value do you mean? When and how did you calculate it?
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