The orqas from comprna

Not much documentation for file headers.

Hi,

could you please provide more information for the validateiso.txt headers?

cds gene n_cds cov_ribo cov_rna f1 f2 ribo_reads pme

Some of these are obvious, but how exactly are cov_ribo and cov_rna calculated? What is f1 and f2?

Thanks,
Alex

ORQAS fails at Ribomap step

I have tried running both the run_ORQAS.sh script and running the pipeline step by step. I have tried using my ownrnaseq and riboseq data and the sample data. I keep getting the same error.

terminate called after throwing an instance of 'std::invalid_argument'
what(): stod
ORQAS/ribomap/scripts/run_ribomap.sh: line 329: 180610 Aborted

Do you have any experience with this error. I have been digging through this for a whole day now. I appreciate any insight!

I verified I am using salmon 0.7.2 for index and alignment as well as STAR 0.4.2j for the riboprof step.
If you suspect it is a software version incompatibility, would you consider making a docker or singularity container?

Thanks for your help!
Alex

(/projects/beck-lab/alex/miniconda/seqtk-env) [nestaa@sumner-log1 ORQAS]$ ORQAS/ribomap/scripts/run_ribomap.sh \
> --rnaseq_fq ${base}/RNA-Seq/GSM3611929_1.fastq \
> --riboseq_fq ${base}/Ribo-Seq/GSM3611926.fastq \
> --transcript_fa ${base}/Iso_BRCA/renamed_cds_sequences.fasta \
> --work_dir ${base}/stepwise/ \
> --offset ${base}/psite.txt \
> --softClipping false \
> --rnaUnstranded true \
> --sailfish_dir ${base}/stepwise/salmon_out
contaminant fasta not provided! Filter step skipped.
skipped filter read step.
aligning reads to transcriptome
aligning RNA_seq to transcriptome...
alignment skipped.
align_reads /pod/2/beck-lab/alex/Breast_Cancer/scripts/ORQAS/RNA-Seq/GSM3611929_1.fastq /pod/2/beck-lab/alex/Breast_Cancer/scripts/ORQAS/stepwise/alignment/GSM3611929_1_transcript_ /pod/2/beck-lab/alex/Breast_Cancer/scripts/ORQAS/stepwise/alignment/GSM3611929_1_transcript_Aligned.out.bam
aligning ribo_seq to transcriptome...
alignment skipped.
align_reads /pod/2/beck-lab/alex/Breast_Cancer/scripts/ORQAS/Ribo-Seq/GSM3611926.fastq /pod/2/beck-lab/alex/Breast_Cancer/scripts/ORQAS/stepwise/alignment/GSM3611926_transcript_ /pod/2/beck-lab/alex/Breast_Cancer/scripts/ORQAS/stepwise/alignment/GSM3611926_transcript_Aligned.out.bam
running riboprof...
cds_range file not provided, assume transcript fasta only contains cds sequences.
getting transcript info...
total number of transcripts in transcriptome: 94317
assigning ribo-seq reads...
constructing profile class...
terminate called after throwing an instance of 'std::invalid_argument'
  what():  stod
ORQAS/ribomap/scripts/run_ribomap.sh: line 329: 180610 Aborted                 /pod/2/beck-lab/alex/Breast_Cancer/scripts/ORQAS/ORQAS/ribomap/bin/riboprof ${options}
pipeline failed at ribosome profile generation!

Determination of uniformity and periodicity thresholds

Dear authors,

I've a question related to the procedure that you followed to classify translated and untranslated ORFs after finishing running ORQAS. How do you exactly determine the cut-off values for the uniformity and periodicity? Also, I've noticed that in Supplementary Figure 1 each different dataset presents different cutoffs, therefore do cutoffs need to be re-calculated for each dataset?

Thanks so much,

Marina

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Not much documentation for file headers.

ORQAS fails at Ribomap step

Determination of uniformity and periodicity thresholds

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