Question: How to check if a Fastq file is contaminated with other strains?
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askif4 • 0 wrote:
I have some Fastq files of the mouse(later mapped to the B6=mm10 reference sequence).
But when I looked at bam files with IGV, some reads were found out to be Rat's (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001895.5)
I have used web Blastn to check some of the reads but it is impossible to check all the reads one by one.
I installed Blastn for Linux but I couldn't figure out how to use it for comparing with limited reference sequences (In my case, I want to compare the reads with only mouse and rat reference sequences)
If you could help me, I would be grateful.
Thank you.
How did you decide that? Did you realign the data to rat genome or just by selecting Rat genome instead of Mouse in IGV? I am surprised IGV allowed you to choose an unrelated genome to view an alignment.
Rat is not a mouse strain but a different species.
Ah, I was searching for the mutation spots with low VAFs. And I found some suspicious reads. So I copied the read sequences and pasted them into web Blastn. That's how I found out that it was contaminated.
It was like this
https://ibb.co/5jD8qtV
Maybe they indeed share some sequences. You can check by mapping reads to mouse and rat ref seqs using bowtie2 , blastn is too slow.
Thank you for your reply, I will try
In addition to what was said, you might also consider to use the BlobToolKit pipeline (paper). I never use it. I just read the paper, but it seems that in case of contamination, it can provide useful insights. Though the other options mentioned seem to be more straightforward to follow.