Primer design not working

[SheetalAmbardar]

SSR markers are identified but primer designing not working. Everytime you select any SSR marker, it shows the error Here jcf7180029229335 is contig name Traceback (most recent call last): File "workers.py", line 113, in run File "workers.py", line 457, in process KeyError: 'jcf7180029229335 does not exist in fasta file'

[lmdu]

Can you send me your sequence file to me for debug.

[SheetalAmbardar]

Dear Dr. Lianming Du,

Please find the attached file (3 GB in size), Kindly let me know once you download it, i will remove it from my drive space. I am able to identify SSR but not able to design primers, it will be great if you can help. cdat_masurca_scf.tar.xz https://drive.google.com/file/d/1YcA4q9Xb7OrizNykK-G629OzTSITqaiJ/view?usp=drive_web

Regards

Sheetal Ambardar Assistant Professor School of Biotechnology University of Jammu Jammu & Kashmir 180006

On Mon, 11 Sept 2023 at 09:35, Lianming Du @.***> wrote:

Can you send me your sequence file to me for debug.

— Reply to this email directly, view it on GitHub https://github.com/lmdu/krait/issues/33#issuecomment-1713127046, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCN7TN35VLTESCPZ4IIVSDLXZ2EXBANCNFSM6AAAAAA4QEBXUM . You are receiving this because you authored the thread.Message ID: @.***>

[lmdu]

Thanks! I have downloaded it.

[lmdu]

I have test Krait v1.5.1 using your data, it works well. You can delete the generated index file with extension of .fxi. And then redo search SSRs.

[SheetalAmbardar]

Dear Dr. Lianming Du,

Thank you for analysing my sequences using krait. Were you able to design primers too.

Regards

Sheetal Ambardar Assistant Professor School of Biotechnology University of Jammu Jammu & Kashmir 180006

On Mon, 11 Sept 2023 at 16:20, Lianming Du @.***> wrote:

I have test Krait using your data, it works well. You can delete the generated index file with extension of .fxi. And then redo search SSRs.

— Reply to this email directly, view it on GitHub https://github.com/lmdu/krait/issues/33#issuecomment-1713639615, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCN7TN3KQTRPFCSYVD3JRPLXZ3UI5ANCNFSM6AAAAAA4QEBXUM . You are receiving this because you authored the thread.Message ID: @.***>

[lmdu]

Yes. Use Krait v1.5.1, and then delete the index file with the same name of sequence file with suffix of .fxi.

[SheetalAmbardar]

Thank you so much. It did worked with new version.

[SheetalAmbardar]

Thank you for troubleshooting this error.