RibORF perl script

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12 months ago

phoenix.sum13 ▴ 90

Hi, I have not used perl this before. What does this error mean? How can I fix it?

rib-seq perl riborf • 734 views

ADD COMMENT • link updated 12 months ago by rpolicastro 13k • written 12 months ago by phoenix.sum13 ▴ 90

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In their documentation they have a reproducible example for this function.

Example commands:

3a. Download an example ribosome profiling dataset from GEO database using the fastq-dump command line (available from the NIH software sratoolkit, https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/).  
fastq-dump -Z SRR1802146 > SRR1802146.fastq

3b. Remove 3’ adapters of sequencing reads.
perl removeAdapter.pl -f SRR1802146.fastq -a CTGTAGGCAC -o adapter.SRR1802146.fastq

You might want to try this to check whether it's the code or your files/command that is causing the error.

ADD REPLY • link 12 months ago by rpolicastro 13k

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Yes, I'm following the documentation, and as far as I can see there is nothing wrong with the code.

ADD REPLY • link 12 months ago by phoenix.sum13 ▴ 90

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You need to run the vignette to make sure their code works. If the vigette doesn't run there is either a bug in their code or there was an installation problem. If it does work that would hint towards a problem with your inputs.

ADD REPLY • link 12 months ago by rpolicastro 13k

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