RiboCode
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xryanglab
release version
Hi, I got a ModuleNotFoundError when testing the RiboCode installation with `RiboCode_onestep -V` Can you help? ``` $ RiboCode_onestep -V Traceback (most recent call last): File "/nexus/posix0/MAGE-flaski/service/projects/data/Bioinformatics/bit_pipe_ribosome_profiling/libraries/venv3/bin/RiboCode_onestep", line 5, in...
Dear RiboCode developers, According to the documentation, it is recommended to include outFilterMultimapNmax 1 parameter in STAR alignment to exclude non-unique alignments and reduce noise for downstream analyses. In case...
When I process metaplots, the log printed that: ========================================================================== No obviously periodicity are detected from bam file SRR22462570/SRR22462570.Aligned.toTranscriptome.out.bam, it could be due to poor quality sequencing. Please check the metagene...
Hi I just wanted to ask for the supplementary R file for the data analysis. I followed the the link but the document is not available anymore. Thanks!
Ribocode does not correctly handle the hdf5 file it creates to store temperary data, resulting in identical results for multiple runs that are ran from the same folder. For example,...
Hi Developers! I am one of the developers of the [nf-core/riboseq](https://nf-co.re/riboseq/dev) pipeline that we have started work on recently. It is now recognised as 'in-development" by the nf-core community but...
RiboCode -a RiboCode_annot -c metaplots_pre_config.txt -l no -g -o RiboCode_ORFs_result Loading transcripts.pickle ... Reading bam file: /n/jobspace/bbcore/schaffer_rpf_abby_min6/two_batches/rpf/alignments_transcriptome/20210125_Index_3_JS8600_S11_R1_001_Aligned.toTranscriptome.out.bam...... Traceback (most recent call last): File "/home/panh/miniconda3/envs/ribocode/bin/RiboCode", line 10, in sys.exit(main()) File "/home/panh/miniconda3/envs/ribocode/lib/python3.7/site-packages/RiboCode/RiboCode.py",...
请问Psites_frame0_RPKM代表的位于0读码框架的reads计算的ORF的表达量吗，不包含读码框1和2的reads
I think I still encounter an issue that is similar to issue#32 i.e., I did not get the psites_number table in the hdf5 file. ``` group name otype dclass dim...
**when i use the metaplots function of ribocode 1.2.14， it show the error:, how can i slove it ,thank you in advance!!!** Create metaplot file and predict the P-site locations...