Question: Plasmodium falciparum SNPS analysis
gravatar for kihugaharrison
9 days ago by
kihugaharrison0 wrote:

I have 29 plasmodium falciparum whole genome sequences that i need to analyse for SNPs. The problem is, each sample contains multiple sequences of upto 768,000 neucleotides....i need to convert this into a single sequence. How do i do this?

genome • 74 views
ADD COMMENTlink written 9 days ago by kihugaharrison0

Can you please try to explain better the data that you have? Show examples, if possible.

ADD REPLYlink modified 9 days ago • written 9 days ago by Kevin Blighe43k

Dear Kevin,

I have raw whole genome sequences 150 bases long that look like this....

ADD REPLYlink modified 9 days ago by Kevin Blighe43k • written 9 days ago by kihugaharrison0

That looks like raw illumina data converted to fasta (with a changed header) and interleaved (R1/R2 following each other).

Are these in one file or you have 29 files? It would be useful to have Q-scores for alignments/SNP calling.

If possible you should acquire original fastq format data and start there.

ADD REPLYlink written 9 days ago by genomax68k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 560 users visited in the last hour