RiboCode

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psite HDF5 file is saved in the wrong location

2

Correct me if I am wrong, but currently, the hdf5 file with psite information is saved in working dir and not in defined output-dir, this makes it fail if output-dir...

Roleren

Read counts issues

2

Is this package only counts the unique mapped reads in the setp "ORFcount"？

tan5251

ValueError: Can't transform the genomic interval, please check!

1

when i use the command "prepare_transcripts",it show "ValueError: Can't transform the genomic interval, please check!",I use the "GTFupdate",it also show the same error,how can i slove this? thanks!

z626093820

prepare_transcripts failed

3

Traceback (most recent call last): File "/home/dr/anaconda2/bin/prepare_transcripts", line 10, in sys.exit(main()) File "/home/dr/anaconda2/lib/python2.7/site-packages/RiboCode/prepare_transcripts.py", line 388, in main processTranscripts(args.genomeFasta,args.gtfFile,args.out_dir) File "/home/dr/anaconda2/lib/python2.7/site-packages/RiboCode/prepare_transcripts.py", line 308, in processTranscripts gene_dict,transcript_dict = readGTF(gtfFile) File "/home/dr/anaconda2/lib/python2.7/site-packages/RiboCode/prepare_transcripts.py", line...

manishbiotechie

Alternative Start Codons

1

Hi, I was wondering how to add an alternative start codon list in the RiboCode step. Thank you for your help! Best, Qidi

qidi-yang

Hi, I was wondering if it will be possible to identify C-terminal extensions using RiboCode. I've noticed that N-terminal extensions / truncations are indeed identified by RiboCode (they fall in...

marcasriv

GTF specification should include start and stop codons

1

I think, the input `gtf` to `metaplots` and `prepare_transcripts` needs `start_codon` and `stop_codon` features in order to recognize something as an annotated CDS; `CDS` features are not enough. Could this...

ewallace

Error when writing transcripts to file

1

Hi, RiboCode runs on my dataset from _Cryptococcus neoformas_, then fails during the writing to gtf. This meant that ORF calling succeeded and wrote a complete .txt file, but for...

ewallace

pickle.load() AttributeError: 'module' object has no attribute 'Gene'

5

Hi, I ran your tool following the guidelines but when I try to run the Ribocode.py bit, I am getting this error: Traceback (most recent call last): File "", line...

ghost

ImportError: No module named Tkinter

2

The Tkinter is needed when import the matplotlib module. If the following error is returned, pls check whether the tkinter package is installed. On Linux platform, users can install this...

zhengtaoxiao