Using CrosscheckFingerprints (Picard) on mice RNAseq data

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Kaoutar Abaakil

• September 18, 2024 13:00
• Edited

Hello, 

I am a beginner at bioinformatics/RNA sequencing data analysis. I have a set of bulk RNAseq data from WT C57BL/6 mice exposed to different diets. I have different tissues collected along the GI tract for each mouse. I am suspecting that there has been a sample swap in one of the tissue type and came across the CrosscheckFingerprints (Picard) tool on your website. I am wondering if it is worth giving it a try for my data as the paper using the tool uses human samples? 

Thank you in advance for your input.  

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  Gökalp Çelik

  • September 19, 2024 22:46

  Hi Kaoutar Abaakil

  Yes it can be used to determine that as well. It does not have to be human samples. 

  Regards. 

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  Kaoutar Abaakil

  • November 12, 2024 10:58

  Hi Gökalp Çelik

  Thank you for your answer. I tried to download an SNP Haplotype map for my strain of mice from EBI website https://www.ebi.ac.uk/eva/?eva-study=PRJEB53906

  However, it seems not to work when I try to use it on my data. It is giving me an error that the file doesn't contain allele frequency. I am unsure if it's something I have to compute on my own or if my haplotype map should have this data already within?

  Best

  Kaoutar

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  Gökalp Çelik

  • November 18, 2024 13:29
  • Edited

  Hi again. 

  Sorry that I was thinking more about intraspecies variation however if tissues are all from a highly inbred species you may not distinguish samples using CrosscheckFingerprints. 

  Regards. 

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