RiboCode

RiboCode copied to clipboard

Hi! I'm sorry to bother you again. I don't know how to deal with different transcripts of one gene when quantification and study 3-nt periodicity in translation. Do you have...

yx-xu

remove PCR duplicate

2

Hi! I'm sorry to bother you. I followed Ribocoed workflow, but I don't know whether need to remove PCR duplicate after STAR alignment. Could you give me some suggestions? Thank...

yx-xu

Dear developers, It seems that the adjusted p values in the collapsed output was calculated from filtered p values. Shouldn't multiple testing correction be done before filtering p-values with the...

mt1022

Empty "transcripts_cds.txt" file

1

Hi, the "transcripts_cds.txt" file generated is empty, how should I fix it? Thanks! Here is GTF ``` A01 phytozomev13 gene 34694907 34695456 . - . gene_id "Gohir.A01G126666.v2.1"; gene_name "Gohir.A01G126666.v2.1"; A01...

huguanjing

Error in GTFupdate

1

Hi, I want to use a special gtf file and want to process these files through `GTFupdate`, but I find that there will be some errors. The following is the...

lbwfff

can't locate attribute: psites_number

1

I'm trying to debug a workflow that runs RiboCode. I tried using the latest container from quay.io and this is the error I'm running into. Any guidance on what I...

trum994

RiboCode_onestep crashes when calling detectORF

1

When trying to use RiboCode_onestep I come across this error below: > Finished reading bam file! > Traceback (most recent call last): > File "/usr/local/bin/RiboCode_onestep", line 10, in > sys.exit(main())...

trum994

error in metaplots step

1

When I run metaplots, it gives an error: ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject I don't know where the...

hugch2020

Whether multiple mapping affect ribocode result

1

Sorry to bother you. I followed your workflow use STAR arguments `--quantMode TranscriptomeSAM` and `--outFilterMultimapNmax 1`,this is the command looks like ``` STAR --outFilterType BySJout --runThreadN 10 --outFilterMismatchNmax 2 \...

Hilarialy

ImportError: cannot import name 'PPoly' from partially initialized module 'scipy.interpolate' (most likely due to a circular import) (/home/zhai2/miniconda3/lib/python3.8/site-packages/scipy/interpolate/__init__.py)

1

when i use the command : metaplots -a -r ,it show ImportError: cannot import name 'PPoly' from partially initialized module 'scipy.interpolate' (most likely due to a circular import) (/home/zhai2/miniconda3/lib/python3.8/site-packages/scipy/interpolate/__init__.py) how...

z626093820