copy number detection from blastn results

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5.3 years ago

tg25 ▴ 20

Hi all,

Before asking this question, I looked on the internet and most of the answers that I can find deal with using lab techniques for cnv detection (which I have done for work that is not related to this question). After searching the Internet, GitHub and reading papers, I cannot find any bioinformatics software that I can use to find cnv's with blastn results. However, I have found software that uses bam files which I don't have since my blast analysis consists of using fasta files.

How can I use blastn results for copy number detection? I used the following code for the blast results so I have a table than I can parse.

blastn -query QueryFasta -subject SubjectFasta -out outFile.txt -outfmt '6 sseqid qseqid bitscore score qcovs qcovus evalue pident nident sstart send qstart qend sseq qseq' -task blastn

I have looked on Biostars and I could not find an answer. I have also looked at so many questions on Biostars, that I might have missed something.

Thanks for the help.

next-gen sequencing blastn cnv • 902 views

ADD COMMENT • link 5.3 years ago by tg25 ▴ 20

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That's because blast algorithm is not designed and or suitable for CNV detection, a simple search on google will guide you to probable thousand papers, tutorials, pipelines of CNV methods.