rnaseqc
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getzlab
Fast, efficient RNA-Seq metrics for quality control and process optimization
hello, Both pip and conda install show different usages as compared to shown on the readme. Conda install : https://anaconda.org/bioconda/rna-seqc usage from conda install: ~/anaconda3/bin/rna-seqc RNA-SeQC v1.1.8.1 07/11/14 Missing required...
Dear all, To prepare the gtf file used in `rnaseqc`, I first converted the gff file to gtf file using following command, `gffread-0.12.7.Linux_x86_64/gffread -T -o out.gtf input.gff`, however it give...
I am using RNASeQC 2.3.5 to evaluate some RNA-seq data. However, in the output *.metrics.tsv file, many metrics are 0/-nan. I paste some lines in my outputs files here. Here...
Hi, I have rnaseq-qc process a batch of targeted RNA-seq data, but I find some genes have "0" coverage in sample.coverage.tsv but definitely not 0 in sample.exon_reads.gct. All my samples...
The "Duplicate Reads" metric is added to the output, however it is never actually calculated. Since there is also a "Mapped Duplicate Reads" metric which is calculated, it would seem...
Hi, I just noticed that in Expression.cpp#extractBlocks method, the line that calculates the end position of alignment block is: block.end = start + current.Length(); // 1-based, closed I'm wondering if...
Is there any equivalent to the legacy version -BWArRNA using bwa to count rRNA reads? That seems to be a more accurate option.
Hi, Thanks for the tool! I recently ran this on a large cohort and noticed some oddities in the output (e.g., end 1 mapping rates > 1 for a subset...
The automatic plots generated are great! I think making at least some of the plots interactive (e.g. using plotly) so users could quickly identify the outlier samples could be very...
Congratulations on reviving this project! All competing RNAseq QC tools have stalled for a long time. Given that most QC metrics produced by omics pipelines seem to converge to MultiQC...
