I have NGS data of TCR-a from probiotic and control group. I want to see if there are identical sequences between these 2 group. In order to do that, I want to find out what are these identical sequences and how many copies are there in each group. My problem is that all my sequences are 250 bases and I can't find a tool that will analyse the sequences the way I want. I have tried QC sequencing report but it only allows me to analyse the first 50 bases. What should I do?
If CLC genomics can't do what I want, can anyone suggest another program?
Try this discussion on biostars,
https://www.biostars.org/p/294514/
You can use seqkit
https://github.com/shenwei356/seqkit
https://bioinf.shenwei.me/seqkit/usage/#common
You can follow
https://www.biostars.org/p/294514/
https://bioinf.shenwei.me/seqkit/usage/#common
Thank you everyone for your suggestion! I have been looking into all the links sent!
Hi, Are you still struggling to run the NGS analysis. If so i can help you..
Ashley - are you working with 250bp reads from a FASTQ file and looking for identical reads? or are you looking for subsequences found within those reads that are shared between the two files?
[BTW - I'm the product manager for CLC @ QIAGEN]
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