Comments (6)
My python version is 2.7.12, should I updated to python 3.7?
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The problem is that your bam file do not have 'MD' tag. Try to generate a new bam file with 'MD' tag.
You do not need to update to python 3.
For STAR, you can set --outSAMattributes All
option.
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Hi, Zhang:
I am just processing the TI-seq data sets generated using LTM. With the Ribo-TISH analysis I noticed in my results, the reads counts at the start codon is only about 10% of the total reads counts. So for your data, How is about this value? Is about 80% or 90% percent of the reads is at start codon?
Thank you!
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Have you got TI-seq quality result using ribotish quality -t option? There's TIS enrich score in the 4th column. Do you mean this value?
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Thank you for your reply.
I used the ribotish quality -t option. That's the enrich score. But I do not think it related to the TIS/total reads. What I mean is that in the LTM data you processed, how many percentage of the reads in the Start Codon compare with the total reads amount. Because I still can see many genes, there is lots of reads along the CDS region. I wondering the LTM works not that efficiency in my experiment.
from ribotish.
The score is calculated as TIS count / average count. It is not the percentage. The actural TIS percentage is not large because the ORF lengths are not short. In fact, it's not easy for LTM to reach high TIS enrich score. Shubin Qian's PNAS LTM data may be the best. Harr is easier, but Harr also has its own problems.
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Related Issues (20)
- Feature Request - Add 3' end match for RPFs HOT 6
- Feature request: Ribo-seq counts in the results HOT 2
- What dose this Horizontal line mean HOT 3
- how to edit the parameter (-d DIS Position range near start codon or stop codon)? HOT 3
- what the types of TisType mean? HOT 2
- ribotish tisdiff error?ZeroDivisionError: integer division or modulo by zero HOT 10
- --altcodons ACG,CUG
- ribotish quality: error: argument -d: expected one argument HOT 2
- ribotish quality "no reads found" for TIS reads HOT 10
- TypeError: '>=' not supported between instances of 'NoneType' and 'float' HOT 3
- TypeError: unsupported operand type(s) for +=: 'NoneType' and 'int' HOT 5
- run mistakes HOT 4
- TypeError: '<' not supported between instances of 'NoneType' and 'int' when running predict module HOT 5
- The meaning and differences in TisType HOT 10
- Wrong CDS annotation HOT 6
- No reads found! HOT 52
- AttributeError: 'Exp' object has no attribute 'sq' HOT 4
- Use of 5' mismatch reads in predict HOT 1
- ribotish predict module run error HOT 2
- ValueError: start out of range (-21) running ribotish quality HOT 4
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