Hello, I have run:
rsem-calculate-expression
on pair end sequencing. From the resulting BAM file mapped to the genome (sample.STAR.genome.bam),...
22 results in 0.0032 seconds.
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rsem: using genome bam for calculating expression
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Incosistent number of paired end reads (BAM file generated by STAR using RSEM)
I have used RSEM to quantify paired-end RNA-Seq data. The alignment was done
using STAR which was called internally by RSEM, using a reference... -
RNA-seq read alignment best practices for low-input Smart-seq2 samples
RNA-seq read alignment best practices for low-input Smart-seq2 samples
Hi All,
I think my data may fall in a nether region between... -
Rsem output interpretation- isoform identification
_________________________________________________________________Last edited by cjgb; 03-14-2017, 11:31 AM. -
How to combine large number of RSEM outputs into a single matrix
Hello All,
I used the STAR aligner to align a bunch of single-cell fastq files and then subsequently ran RSEM for quantification. Now I... -
GFF3 formatting wrong for RSEM?
Hello SEQanswers community,
When I run rsem-prepare-reference with refseq it only captures "tRNA" in my gff3 file. I only realized... -
RSEM bam question
Hi, I used RSEM with STAR. I noticed that in the RNAME field of the BAM (3rd filed) , where usually had e.g chr1 now I have the name of the isoform. With... -
TPM and FPLM problem?
Hi
I have used Illumina hiseq 2000 to sequence two samples (two organs of a plant) without replication. I know that without replication I can not...Last edited by Ahmadiut; 06-24-2016, 04:08 AM. -
RSEM prep error
Hi! I'm new to bioinformatics and I'm learning the ropes.
I'm trying to estimate abundance following the Trinity-RSEM pipeline. My script... -
RSEM with HISAT2
Hello guys,
I have RNA-sequencing data of around 250 patients with leukaemia.
I have built up a basic pipeline using HISAT2 as... -
strand-specificity in RSEM
Hello,
I'm trying to figure out the settings for analysing strand-specific RNA-Seq data from Illumina TruSeq chemistry with rsem-calculate-expression... -
Problem using the Trinity script align_and_estimate_abundance.pl with RSEM
Hi,
I have assembled RNA-Seq data do novo in Trinity, and am now trying to estimate the abundance of the transcripts that were identified. I used... -
Comparative expression analysis across two species
Hello everyone!
I have the following situation/design that I could use some help figuring out the best way to analyze:
I... -
Intrasample exon analysis of RNA-Seq data using RPKM values
Hello SeqAns community,
I have been using Mapsplice and RSEM to analyze RNA-Seq data.
The output of my pipeline are the expected... -
rsem-calculate-expression takes very long with paired-end reads (using bowtie2)
I am want to use RSEM for transcript quantification. I have paired-end Illumina 1.5 encoded fastq files, a genome file, and a gtf file from Ensembl....
