Question: copy number detection from blastn results
gravatar for tg25
12 months ago by
tg250 wrote:

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.

sequencing cnv blastn next-gen • 262 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by tg250

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.

ADD REPLYlink written 12 months ago by Buffo1.8k

Thank you for your help.

ADD REPLYlink written 12 months ago by tg250
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