ribotish

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TypeError: unsupported operand type(s) for +=: 'NoneType' and 'int'

7

`ribotish predict -b ${bams} -g ${gtf} -f ${fa} -o ${res_dir}/longest_pred.txt -p 40 --longest -v -v` after run this code, I got the following error  How can I deal with...

haowBio

AttributeError: 'Exp' object has no attribute 'sq'

4

Hi, I am trying to run ribotish on human samples with older genome and annotation (gtf) from 2014. This is the command I ran: ``` ribotish predict \ -b file.bam...

noepozzan

The meaning and differences in TisType

10

Dear developer, Good day. Thank you for your development and maintenance of this software. I was wondering if you could explain about the definitions of different classes of `TisType`? I...

ruixuan-zhang

Wrong CDS annotation

6

Hello, I have ran: ribotish predict -t TIS_bams_new/R3_ProAligned.sortedByCoord.out.bam -b CHX_bams_new/R3_ProAligned.sortedByCoord.out.bam -g gencode.v19.annotation.gtf -f GRCh37.p13.genome.fa -o pred.txt --framebest The result is that (It is not finished): No offset parameter file found...

agsanbel

run mistakes

4

Traceback (most recent call last): File "/gss1/home/zpchen/miniconda3/envs/ribotish/bin/ribotish", line 56, in main() File "/gss1/home/zpchen/miniconda3/envs/ribotish/bin/ribotish", line 34, in main commands[cmd].run(args) File "/gss1/home/zpchen/miniconda3/envs/ribotish/lib/python2.7/site-packages/ribotish/run/quality.py", line 85, in run cdsBins = args.bins, numProc = args.numProc,...

czppeter

ribotish quality: error: argument -d: expected one argument

2

Hi, when I wanted to use option -d to define the position range near start codon or stop codon, I met such an error: ribotish quality: error: argument -d: expected...

yycunc

ribotish tisdiff error?ZeroDivisionError: integer division or modulo by zero

10

hi,when I use the ribotish tisdiff ,some error information as follows: my command : ribotish tisdiff -1 pred1.txt -2 pred2.txt -a v1.sort.bam -b vi2.sort.bam -g test.gtf -o diff -v error...

etmorefish

Feature request: Ribo-seq counts in the results

2

Thank you for the great tool! It seems to be working perfectly for me but I would like to request a feature implementation. Would it be possible to add a...

nsotta

Visualization of single transcripts with a-site/p-site coverage

4

Hello! First of all thank you for developing Ribo-TISH! I have found it really useful for the QC it provides and also for uORF prediction. I have a question that...

AlexFryd