blat the RNAseq data of organoids generated from mouse

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6.5 years ago

alireza346 ▴ 10

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?

RNA-Seq • 899 views

ADD COMMENT • link 6.5 years ago by alireza346 ▴ 10

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

ADD REPLY • link 6.5 years ago by GenoMax 147k

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yes the adapters are trimmed

ADD REPLY • link 6.5 years ago by alireza346 ▴ 10

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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.

ADD REPLY • link 6.5 years ago by GenoMax 147k

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