Quantification after creating an index supplemented with bam files produces NAs in evens of interest

[sopenaml]

Hi,

I'm interested in quatifying the PSI of a 5' splice site in a particular gene. The event is not in my annotation, but I can see that it's used in my bam files (on IGV). So I've decided to use the option of creating an index supplemented with bam files. The step works, as I can see nodes for the area of interest but when I try to quantify my files, the node of interest (searched by coordinates) appears as NA and no values in any of the other columns. Would anyone know why that is and how can I get whippet to produce those values?

Thanks

[Alex-Nesta]

I think you will see NAs if there are not enough reads at the splice junction to accurately quantify the splicing event. Can you check your bam in IGV to see if you have any split reads aligning to the region of interest?

Hope that gives you some ideas. Alex

[sopenaml]

Thank you for your answer. There are split reads that I can see on IGV and I don't think there are few, see attached picture. The exon of interest is the one in the center-left part of the attached picture. The splice variant I'm interested is the A5'ss that is being used in samples coloured in red, blue, green and orange, while the annotated one is the full exon used in the brown and purple track.

Any insigths in why whippet doesn't provide quantification for such event would be greatly appreciated.

Kind regards,

Miriam

---

From: Alex Nesta [email protected] Sent: Friday, April 3, 2020 5:36 PM To: timbitz/Whippet.jl [email protected] Cc: Miriam Llorian Sopena [email protected]; Author [email protected] Subject: Re: [timbitz/Whippet.jl] Quantification after creating an index supplemented with bam files produces NAs in evens of interest (#98)

I think you will see NAs if there are not enough reads at the splice junction to accurately quantify the splicing event. Can you check your bam in IGV to see if you have any split reads aligning to the region of interest?

Hope that gives you some ideas. Alex

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftimbitz%2FWhippet.jl%2Fissues%2F98%23issuecomment-608540761&data=02%7C01%7C%7C8cbf3952a6364df79da508d7d7ed2164%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637215285786317771&sdata=Ija0YSb3p7mVew3oy2ax0lJPbYMSjY%2BkJaiHVEmopJw%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAGLEBWLPELSTPFUESQRCO3LRKYF77ANCNFSM4LPGTG5Q&data=02%7C01%7C%7C8cbf3952a6364df79da508d7d7ed2164%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637215285786327769&sdata=kSIZxJF84nFfUDTOn6SmcWrmTrCuzYE3P6jhacq%2BkqQ%3D&reserved=0.

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[sopenaml]

Hi,

Sorry to bother you, but I was wondering if you have received my message and had any insights as to why whippet does't quantify the splicing event I'm interested on?

Thank you very much for your time and help,

Kind regards,

Miriam

---

From: Miriam Llorian Sopena [email protected] Sent: Monday, April 6, 2020 1:32 PM To: timbitz/Whippet.jl [email protected] Subject: Re: [timbitz/Whippet.jl] Quantification after creating an index supplemented with bam files produces NAs in evens of interest (#98)

Thank you for your answer. There are split reads that I can see on IGV and I don't think there are few, see attached picture. The exon of interest is the one in the center-left part of the attached picture. The splice variant I'm interested is the A5'ss that is being used in samples coloured in red, blue, green and orange, while the annotated one is the full exon used in the brown and purple track.

Any insigths in why whippet doesn't provide quantification for such event would be greatly appreciated.

Kind regards,

Miriam

---

From: Alex Nesta [email protected] Sent: Friday, April 3, 2020 5:36 PM To: timbitz/Whippet.jl [email protected] Cc: Miriam Llorian Sopena [email protected]; Author [email protected] Subject: Re: [timbitz/Whippet.jl] Quantification after creating an index supplemented with bam files produces NAs in evens of interest (#98)

I think you will see NAs if there are not enough reads at the splice junction to accurately quantify the splicing event. Can you check your bam in IGV to see if you have any split reads aligning to the region of interest?

Hope that gives you some ideas. Alex

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftimbitz%2FWhippet.jl%2Fissues%2F98%23issuecomment-608540761&data=02%7C01%7C%7C8cbf3952a6364df79da508d7d7ed2164%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637215285786317771&sdata=Ija0YSb3p7mVew3oy2ax0lJPbYMSjY%2BkJaiHVEmopJw%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAGLEBWLPELSTPFUESQRCO3LRKYF77ANCNFSM4LPGTG5Q&data=02%7C01%7C%7C8cbf3952a6364df79da508d7d7ed2164%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637215285786327769&sdata=kSIZxJF84nFfUDTOn6SmcWrmTrCuzYE3P6jhacq%2BkqQ%3D&reserved=0.

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT