Searching for specific sequences in WGS data
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!
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what sequences do you have?? are they read sequences? How did you get genome file in bam format??
They are nucleotide sequences. I got bam file from the guys, who performed the experiment. This is the only file I have for each of the genomes I want to study.
bam (binary of sam) is usually generated after aligning sequences to reference sequence using mapper like bowtie or bwa etc. was this bam generated after aligning nucleotide sequences you wish to check?? i
I guess - yes. I see here https://www2.warwick.ac.uk/fac/sci/statistics/staff/academic-research/nichols/presentations/ohbm2014/imggen/Nho-ImgGen-WGSeqPractical.pdf that it is a standard situation when NGS company provides bam files and they can be converted back to fastq
Convert BAM to .fastq ot FASTa and then can go whatever you like !!
Could you please suggest the tool that can identify the presence/absence of the sequences in fastq files?
If the bam is generated using sequences you wanted to check, in bam 3rd column should not be *(star). Those are sequences not in your genome
Thank you very much!
Hello valerie!
It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=72119
This is typically not recommended as it runs the risk of annoying people in both communities.