TypeError: unsupported operand type(s) for -: 'str' and 'int' (DegNorm)

[KosarHooshmand]

Hey,

I am currently running DegNorm (version 0.1.4) on SRA samples using gencode_v31_annotation.gtf file.

I am facing error in DegNorm (11/12/2019 07:44:27) ---- Determining gene overlap structure across chromosomes, stag.

Error_type:

GTF file format:

Is this error correlated with GTF file?

I would appreciate any help from your side.

Thanks, Kosar

[ffineis]

Hello Kosar,

Thanks for using DegNorm, I will get back to you over the weekend.

[KosarHooshmand]

Hello Kosar,

Thanks for using DegNorm, I will get back to you over the weekend.

Thanks . Also, another question. I've aligned fastqs against gencode annotation file using kallisto. As you may know, kallisto outputs are pseudo-bam-aligned. Am i going to face any problem running DegNorm on pseudo bam files?

[KosarHooshmand]

Hello Kosar, Thanks for using DegNorm, I will get back to you over the weekend.

Thanks . Also, another question. I've aligned fastqs against gencode annotation file using kallisto. As you may know, kallisto outputs are pseudo-bam-aligned. Am i going to face any problem running DegNorm on pseudo bam files?

---

I've also aligned my fastq files using STAR, but still getting the same Error

[ffineis]

Kosar -

I am unfamiliar with kallisto and pseudo-bam files, but your issue is with the .gtf file. It appears as though the start field in the .gtf is coming in with string values in it. Can you please send over the .gtf?

Thanks, Frank

[KosarHooshmand]

Kosar -

I am unfamiliar with kallisto and pseudo-bam files, but your issue is with the .gtf file. It appears as though the start field in the .gtf is coming in with string values in it. Can you please send over the .gtf?

Thanks, Frank

Hey Frank,

thanks for your reply. Everything is working fine now.