-
The content of the *Log.final.out file generated by STAR is valuable for QC purposes. Can it be retained as part of the QC output in the RNA-Seq CGL pipeline? If you want to wait until we do a broader…
-
Dear sir,
When I ran "rsem-calculate-expression --paired-end --alignments -p 8input.bam" gencodev22 ./out.
I got error message
rsem-parse-alignments ../bowtie2/hg38 ./rsem-out.temp/rsem-out ./rs…
-
For GTEx V7 data we've done imputation and rna-seq normalization, and we have PCA analysis results from Broad. PEER analysis is still running. Once we have the result we should have the material to do…
-
Experiment Type:
RNA-Seq
Sequencing of total cellular RNA
Workflow Management:
Bash/SLURM
Scripting and job scheduling
Software Stack:
FastQC
MultiQC
STAR
RSEM
samtools
DESeq2
What …
-
Hello Developers,
I predicted the plant genome and obtained about 48,000 and 70,000 genes using braker and funannotation pipeline RNA-seq and protein, respectively. Other people did another genome …
-
Experiment Type:
RNA-Seq
Sequencing of total cellular RNA
Workflow Management:
Bash/SLURM
Scripting and job scheduling
Software Stack:
FastQC
MultiQC
STAR
RSEM
samtools
DESeq2
What …
-
Experiment Type:
RNA-Seq
Sequencing of total cellular RNA
Workflow Management:
Bash/SLURM
Scripting and job scheduling
Software Stack:
FastQC
MultiQC
STAR
RSEM
samtools
DESeq2
What …
-
Hello there,
I am very excited to start using kallisto with some of our bulk, long-read RNA seq data. For the analysis I am conducting, I wanted to use kallisto to quantify read counts, and then us…
-
Hi,
Just wanted to check the normalisation of some of the output files. From the output documentation:
"The number of reads aligned to the spike-in genome are then used to calculate a scaling fac…
-
Experiment Type:
RNA-Seq
Sequencing of total cellular RNA
Workflow Management:
Bash/SLURM
Scripting and job scheduling
Software Stack:
FastQC
MultiQC
STAR
RSEM
samtools
DESeq2
What …