Regarding output of nanosplicer (missing BED file)

[PRIYANKA-22091995]

Hello Team,

I have got the nanosplicer output, but it is only the tsv file, there was no bed file generated. What is the reason for that.
The other question i have from the tsv file, based on the tsv file headers, should i consider the JAQ score or the SIQ score for the prediction of the splicing junction.
It would be nice to have your comments on the same.

Thanks & Regards
Priyanka Roy

[youyupei]

Hi @PRIYANKA-22091995,

Thanks for being interested in NanoSplicer. For the bed output, would you be about to run the example script (script.sh under example) and check whether you can get the .bed. I can't be certain at the moment without further information but if you could get the bed from the example, I assume the reason you didn't get the .bed was because the program has NOT been finished successfully, you could send me any command line output/error message you got .

For the downstream usage, generally results with higher JAQ , higher SIQ, and higher "best_prob" tend to be more accurate. When you have enough reads, I would recommend filtering some results to get more confident results (usually JAQ > 0.95 SIQ > -0.4 and best_prob>0.95 will mean confident results, but you could adjust the number based on your depth).

Regards,
Yupei

[PRIYANKA-22091995]

Thanks for your response. For the downstream usage, I don't have any SIQ > -0.4 threshold, but I have JAQ > 0.95 and best_prob> 0.95.So, should I process with these parameters, excluding the SIQ > -0.4 threshold? Will that be suitable for the analysis of alternative splicing events.It would be nice to have your insights on the same. Thanks & Regards Priyanka Roy

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On Tue, Dec 5, 2023 at 5:29 AM Yupei You ***@***.***> wrote: Hi @PRIYANKA-22091995 <https://github.com/PRIYANKA-22091995>, Thanks for being interested in NanoSplicer. For the bed output, would you be about to run the example script (script.sh under example) and check whether you can get the .bed. I can't be certain at the moment without further information but if you could get the bed from the example, I assume the reason you didn't get the .bed was because the program has NOT been finished successfully, you could send me any command line output/error message you got . For the downstream usage, generally results with higher JAQ , higher SIQ, and higher "best_prob" tend to be more accurate. When you have enough reads, I would recommend filtering some results to get more confident results (usually JAQ > 0.95 SIQ > -0.4 and best_prob>0.95 will mean confident results, but you could adjust the number based on your depth). Regards, Yupei — Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A2FSZXTHXHSBQ43N5VVU5E3YHZPW5AVCNFSM6AAAAABAGHM3ZGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZZG43DONZVGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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[youyupei]

I would highly recommend putting an SIQ threshold. It indicates whether or not the squiggle used to characterize the junctions is informative.
However the threshold doesn't have to be -0.4, I think you could relax it to ~-0.8.

[PRIYANKA-22091995]

Thank you so much for making it more clear.

Thanks & Regards
Priyanka Roy