Hi there,
I have recently assembled a NGS data and to see if it is currect, a company has assembled it for me. Two results are 99% identical with e-value of 0. However, I have almost 4kb extended genome containing an putative coding sequence. The files sent by company is reduced in size and I think it has trimmed into smaller files. Now, i do not know which one should be taken for further analysis. I seek for your recommendations.
Regards
Alireza
Dear Alireza
Check the read quality of the fastq file using FastQC (or NGS QC toolkit). A read having low quality usually trimmed using trimmomatic tool (that's way file sizes are been reduced). Finally you can go for assembly.
However, it is very difficult to say, without analyzing the read data, which one is better.
Regards
Mohammad
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103590/
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3270013/
Hi dear Mohammad,
I've checked NGS quality using FastQC the company has also checked as the same. However, the Q30 quartiles in both ends of the company result seems trimmed and reduced significantly in in comparison with my result.
I think you should move on with yours, if you are worried / not sure about their procedure. You can review your assembly anytime, anyway.
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