How to handling Transcripts without strand information in IsoQuant GTF File

[bxZhang996]

Hi,

First, I want to express my appreciation for the IsoQuant tool; it has been incredibly helpful and has saved me a lot of time.

I have a question regarding the GTF file generated by IsoQuant. I noticed that some transcripts in the file are missing strand information, as shown in the screenshot below:

Could you please help me understand why these transcripts lack strand information( strand show ".")? Also, what would be the best way to handle these transcripts?

Any guidance would be greatly appreciated.

Thank you very much!

Best regards,
Zhang

[andrewprzh]

Dear @bxZhang996

Thank you for the feedback!
Could you please share the log and your IsoQuant version?

Best
Andrey

[bxZhang996]

Hi, @andrewprzh

In my samples, most transcripts do have strand information; however, a small number of transcripts are missing this information. I have extracted these transcripts and included them in the attached file:
Adipose20-1_without_strand.txt

Additionally, here is the log file from running IsoQuant on the sample:
isoquant.log

In most of the samples I processed, there were a few transcripts missing strand information.

Thank you for your help!

Best regards,
Zhang

[andrewprzh]

Dear @bxZhang996

You are using version 3.3.1, which was released more than one year ago. The issue with . strand in transcripts was fixed in version 3.4.

Best
Andrey