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MingyuYang-Yale / DBiT-seq

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Hi, I have some problem about SRA-uploaded fastq file. #2

Closed dmsalsgh97 closed 3 years ago

dmsalsgh97 commented 3 years ago

Hi, I'm trying to understand the library structure of DBiT-seq. I downloaded the 0725e10cL sample(SRA Acession: SRR10182230) from the GEO(GSM4096262).

In the SRR10182230_1.fastq, Read1 only has 26base length sequences like below. image In my think, it is a fully re-formatted structure containing Barcode B(8bp) - Barcode A(8bp) - UMI(10bp)

Then, What is Read2? In the SRR10182230_2.fastq, I couldn't find what the Read2 it is. image

Below is my understandings of DBiT-seq library structure and the seqeucing... image Is it right? If it is right, Read2 in the SRR10182230_2.fastq should contain the cDNA of captured mRNA.

Thanks for sharing your effort!

MingyuYang-Yale commented 3 years ago

Yes, you are totally right. Read2 contains the cDNA of captured mRNA.

Best, Mingyu

============================= Mingyu Yang, Ph.D. Postdoctoral Associate in Fan lab Department of Biomedical Engineering Yale University 55 Prospect St. MEC 103B New Haven, CT, 06511

T: +1(203) 361-8885 E: mingyu.yang@yale.edu

On Jan 6, 2021, at 4:59 AM, dmsalsgh97 notifications@github.com wrote:

Hi, I'm trying to understand the library structure of DBiT-seq. I downloaded the 0725e10cL sample(SRA Acession: SRR10182230) from the GEO(GSM4096262).

In the SRR10182230_1.fastq, Read1 only has 26base length sequences like below. https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F42495757%2F103751223-4c6e5300-504b-11eb-9a88-4149938101bc.png&data=04%7C01%7Cmingyu.yang%40yale.edu%7Ceee3b27f4785471a35a408d8b229d079%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637455239948984793%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=28FK%2FHOUA981MWQBQUNIkmr8Qs8t5d5EPGfPoBIY97E%3D&reserved=0 In my think, it is a fully re-formatted structure containing Barcode B(8bp) - Barcode A(8bp) - UMI(10bp)

Then, What is Read2? In the SRR10182230_2.fastq, I couldn't find what the Read2 it is. https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F42495757%2F103751837-3d3bd500-504c-11eb-88cd-1bd77d84b11d.png&data=04%7C01%7Cmingyu.yang%40yale.edu%7Ceee3b27f4785471a35a408d8b229d079%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637455239948984793%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=zlR3rFKHmSKl3P2HaiYsQz9xooOeEHaVq%2BBGTc9yxsQ%3D&reserved=0 Below is my understandings of DBiT-seq library structure and the seqeucing... https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F42495757%2F103755359-0b793d00-5051-11eb-9a76-080a6b6fe783.png&data=04%7C01%7Cmingyu.yang%40yale.edu%7Ceee3b27f4785471a35a408d8b229d079%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637455239948994783%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=nM1UdWk1ZjQVKRtaueXokZ6fhM%2FsGD2fqNbJaeK7Ehs%3D&reserved=0 Is it right? If it is right, Read2 in the SRR10182230_2.fastq should contain the cDNA of captured mRNA.

Thanks for sharing your effort!

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dmsalsgh97 commented 3 years ago

Thanks. your comment was really helpful!