Question: copy number detection from blastn results
0
gravatar for tg25
9 weeks ago by
tg250
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 • 137 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by tg250
1

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 9 weeks ago by Buffo1.7k

Thank you for your help.

ADD REPLYlink written 9 weeks ago by tg250
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