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searching for specific RNA nucleotide sequences

I have a unique chimera RNA nucleotide sequence. Is there a script I can use to to search my RNA seq bam files for that specific nucleotide motif.

rna-seq
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updated by wm wm • written by Adeler001 • Adeler001

1 answer

If you just want the reads containing the specific sequence, you could use grep;

$ samtools view in.bam | grep 'your sequence' > out.sam
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written by wm wm

And grep the rev comp

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written by swbarnes2 swbarnes2

thanks for the reply . is there a way to a call sequence that has a specific nucleotide pattern for most reads but may alter in this pattern by 3 or 5 nucleotide for other reads?

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written by Adeler001 • Adeler001

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