searching for specific RNA nucleotide sequences

Question

[Adeler001]

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.

Answer 1

[wm]

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

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

[swbarnes2]

And grep the rev comp

[Adeler001]

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?