Wrong coverage

[wynstep]

Dear all,
I am facing an issue with gemBS map that I hope you can help solving/addressing.
Essentially I tried to calculate the depth of a BAM file generated after the "map" command (union of 2 lanes), then comparing with BSmap (the standard tool in my lab).

With BSMap [I know the coverage is respect the declared range]:

With gemBS:

I also noticed the BAM generated with gemBS is (almost) double the size of the BSMap. Do you have any suggestion for me?
Many thanks

Stefano

[heathsc]

Can you send a fragment of the BAM file from gem and from BSMap (with the same reads)? Simon

…

On Wed, 25 Mar 2020, 19:45 Stefano Pirrò, ***@***.***> wrote: Dear all, I am facing an issue with gemBS map that I hope you can help solving/addressing. Essentially I tried to calculate the depth of a BAM file generated after the "map" command (union of 2 lanes), then comparing with BSmap (the standard tool in my lab). With BSMap [I know the coverage is respect the declared range]: [image: 111056 mean barplot] <https://user-images.githubusercontent.com/7643476/77573377-801b2a80-6ec8-11ea-8c59-be8298c44214.png> With gemBS: [image: 111056 mean barplot] <https://user-images.githubusercontent.com/7643476/77573493-aa6ce800-6ec8-11ea-9371-886ce1eb4b8b.png> I also noticed the BAM generated with gemBS is (almost) double the size of the BSMap. Do you have any suggestion for me? Many thanks Stefano — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#75>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAY4653HUYOSBZDHCXK766TRJJGOLANCNFSM4LTVOZ4Q> .

[wynstep]

Hi there, thanks fro your reply.
I extracted the same region (chrX:66763874-66950461) AR gene, from both BAM files:

AR_coords.zip

many thanks

[wynstep]

Hello! Any update/suggestion on this issue?