How to find same sequences between two sequencing project

[czq2007hlj]

Hello, I have two tables of sequences, one from DNA seq, one from RNA seq. Is there a easy way for me to it find the same sequences in both tables?


I used the same individuals for DNA seq and RNA seq. Now I want to match the individuals using same SNPs in both project.

Thanks for the help.

[blancha]

Your question is difficult to understand, but I am assuming you are trying to compare SNPs found in RNA-Seq data to SNPs found in DNA-Seq data.

For individual genes and SNPs, you could compare the datasets visually by loading the BAM files or the VCF files in IGV.

For a genome wide comparison, you can just compare the mutations in the VCF files or the data from the VCF files converted to an Excel file.
There has to be some manual curation, and cutoffs set for the RNA-Seq data. The coverage will be uneven for the RNA-Seq data, and, amongst other issues, indels may not be handled properly.

[GenoMax]

If you actually have data in "tables" then perhaps you only have a reduced representation of the data (unless you are referring to a VCF file is tab-delimited).

If that is the case then you could use vcftools/bedtools "intersect" to find the SNP's that are common in both files. All caveats mentioned by @blancha still apply.

Hopefully you know "what data is what" and are only planning to match the SNP's as additional QC confirmation for the samples.