scikit-ribo

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Hi guys - to double check some of my own work, I've been trying to compare it to scikit-ribo's estimates of predicted protein abundance (PA). If I read the paper...

zslastman

RNAfold / pre-built files for human

12

Hi, I'm testing scikit-ribo on a set of ribo-seq experiments from human cancer cell lines. I am experiencing the same issue reported by @aemoor some months ago while running gtf_preprocess.py...

matteobenelli

Incorrect codon files generated by scikit-ribo-build for mm10

1

I have been trying to use scikit-ribo on mouse ESC Ribo-Seq data but the output files generated from scikit-ribo-build do no correctly parse the given input GFF file. I am...

nabeel-bioinfo

Hi, I installed scikit-ribo using pip and am using it with human data. In order to generate the RNA fold file, I am first running gtf_process.py on our GTF file...

catsargent

Whilst using gtf_preprocess.py to create the expandCDS.fasta file, I obtained the following error: Traceback (most recent call last): File "/usr/local/lib/python3.5/dist-packages/scikit-ribo/gtf_preprocess.py", line 280, in worker.getSeq() File "/usr/local/lib/python3.5/dist-packages/scikit-ribo/gtf_preprocess.py", line 154, in getSeq...

catsargent

gffutils error for bed12 conversion in scikit-ribo-build.py

1

Hi there, I am trying to test scikit-ribo on some yeast ribo-seq data we have just generated. When running scikit-ribo-build.py I get the following error: `File "/home/drew/anaconda3/envs/scikit-ribo/lib/python3.6/site-packages/gffutils/interface.py", line 227, in...

drewjbeh