Analyzing Whole exome Seq for mouse

Question

[Assa Yeroslaviz]

I have a WES data set with two PE biological replicates. I am trying to follow this specific workflow. But I keep getting into problems. The biggest one is that this pipeline was set to work with human data. So I can't even get all the data.

I was wondering if there are any specific pipelines/workflow for Whole Exome Sequencing, which are either mouse-specific or not org.-specific at all.

Concerning the above mentioned pipeline - where can I get the exome target capture file (bed format) from?

thanks

[Assa Yeroslaviz]

Hello Assa Yeroslaviz!

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[ATpoint]

Please do not close questions. I moved two omments to answer which you can mark as accepted if they solved the question. You can accept more than one answer.

Answer 1

[ATpoint]

where can I get the exome target capture file (bed format) from

From the company who made the capturing probes.

[Assa Yeroslaviz]

thanks for both answers. Does this file kit and organism specific?

[ATpoint]

Sure, mouse complementary sequences for mouse genome, human complementary sequences for human genome etc.

[Assa Yeroslaviz]

When I'm looking at the Nextera file for example, They only offers files for human exome. Does it means that they do offer a kit at all for mouse?

[ATpoint]

I don't know. Which kit was used for your data?

[Assa Yeroslaviz]

I'm still trying to figure it out.

[Assa Yeroslaviz]

ok, the kit is from Agilent Mouse exome capture library

Answer 2

[GenoMax]

This one seems to be generic for use with any genomes.

where can I get the exome target capture file (bed format) from?

If you know what kit was used then you should be able to get that file from kit manufacturer.

[Assa Yeroslaviz]

As some other files are missing, are there any other pipeline worth testing? thanks