blat the RNAseq data of organoids generated from mouse

Question

[alireza346]

I have RNAseq data from organoids were generated from mouse. I tried to blat many of the reads on UCSC (against mm10 genome) but I got this error: "Sorry, no matches found". the reads were selected from different parts of the fastq files. do you know what the problem could be?

[GenoMax]

What is length of the reads your are blating? Have then been scanned/trimmed for presence of adapters?

[alireza346]

yes the adapters are trimmed

[GenoMax]

Then you should use blast at NCBI to make sure the reads are still mouse. You did not mention what was the range of read lengths. blat only works well with sequences longer than ~25 bp.