for duplicated read names -> having "dup" on gtf output, but not on SAM/FASTA output about sqanti2

[Magdoll]

Hi @yejilee-biostat ,

It was my original intention to keep just one record name for SAM and FASTA. GFF and Classification does not allow duplicate read names but it's acceptable for SAM.

I'll add a feature request for SQANTI2 to handle duplicate read names for FASTA/SAM. However note this will only be added to the latest version of SQANTI2 I'm developing which will be on Python3.

-Liz

[yejilee-biostat]

Thanks a lot again, Liz! I will wait for the updated version SQANTI2 then :) !!

[yejilee-biostat]

Hi Liz,

I see you have updated SQANTI2 - can I assume that now there is no duplicated read names on SAM and FASTA output?

[Magdoll]

No still working on it - I will close this issue and note the version that supports this when it's fixed. Sorry and thanks for your patience.

[yejilee-biostat]

I see - thanks again for kind reply!

[18217639506]

Hi Liz,
I got the same issue when use the SQANTI2. I see you have updated SQANTI2 for many versions. Can I assume that you have solved the issue about duplicated read names on SAM and FASTA output?

[Magdoll]

Hi @18217639506 ,sorry not actually i have not resolved this issue yet. If you want to help, could you send me some test data?
-Liz

[Karthickrishnan]

Hi Liz,

I have used SQUANTI3, I have this issue in that version too.
Should I use any particular version of SQUANTI2??

[Magdoll]

Hi @Karthickrishnan ,
Actually neither SQANTI2 nor SQANTI3 has this issue solved. I need some test data ...would you be willing to share the data confidentially so I can try to code something up? If yes, please give me an email to send data upload request to.
Thanks!
-Liz

[Karthickrishnan]

Thank you very much for your reply Liz.
My Email id is [email protected]. I guess you can also use this data for ConesaLab/SQANTI3#5.

[Magdoll]

Hi @Karthickrishnan , a file upload request has been sent. Please provide the input GTF (not fasta), the commands used, and if you are using a non-human/mouse genome/annotation point me to the location where I can download it. Thanks!
-Liz