Searching for specific sequences in WGS data

[Kogan]

Hi everyone.

I have never worked with WGS data and have a question. I have several thousands of sequences that I can convert in any format (e.g. fasta file) and I want to know whether each of the sequences in presented in my genome. Just 'yes' or 'no' for each sequence and, if it is possible, number of repeats for each sequence if it is presented in genome (e.g. presented twice or three times). I have both fastq and bam files. It is human genome.

I went through several presentations, but would be grateful if someone who has an experience in WGS data could suggest me the procedure/pipeline.

Thanks!

[finswimmer]

What do you mean by "I have both fastq and bam files"? Is this realated to your "several thousands of sequences" or your genome?

If it's the first than you already have a file were all your sequenced were tried to mappe to a reference (was this your genome?). You can use than use samtools to asked how many reads are mapped.

samtools view -F 0x4 -c mybamfile.bam

or

samtools flagstat mybyfile.bam

fin swimmer