Hi,
I am analysing yeast strains NGS results containing amplicons for fragments of genes. I've mapped reads to whole genome S288C and EC1118. I compared the results. One amplicon were mapped to fragment of gene A in S288C reference. This amplicon matches in reference coordinates for gene A. The lenght of amplicon is 600bp.
I've done the same thing to EC1118 reference and I've discovered that this amplicon were mapped to about 75% of the same fragment of gene A. The mapping results showed that reads were shifted about 150bp. (and cover intron sequence).
Gene A has different coordinates in references and I took this into analysis.
Why do I have displacement in results?
Could it be caused by some kind of rearrangements?
I would really appreciate for help. Best, Agata
0 answers
No answers yet.
Log in to answer this question.
-
warning[vg::giraffe]: Cannot cluster reads with a fragment distance smaller than read distance
written by cassiwatt •
-
Amplicon sequencing and unwanted amplicons
written by misterie
-
BWA or STAR for RNAseq?
written by agata88
-
De novo RNAseq analyses
written by agata88
-
How reads are divided into taxonomy level in Qiime?
written by agata88
-
Yeasts references SGD and Ensembl
written by agata88
-
Different results of bwa mapping for one file and multiple files
written by agata88
-
How to map by bwa with 50 mismatches?
written by agata88
-
tophat output summary
written by agata88
-
normalization of NGS results
written by agata88
Do you have paired end data? Does one end of the amplicon end in intron sequence?
This is just speculation but it is not improbable to imagine that your lab strain may be subtly different from published references because of its age/handling (especially if it has been some years since it was originally acquired).
Yes, I have PE reads and one end of amplicon ends in intron sequence and second ends in gene.
In that case I would expect the same results for S288C reference, I think. Do you think that this displacement could be caused by insertion? But the amplicon length is 600 in both cases ...so nope. Any other idea?
Ok, But insertion/deletion can be in nearest area, like in other gene! In that case my whole amplicon will move. Because I see that all reads were moved in left I think this may be caused more possibly by deletion. Correct me if I am wrong, please. Agata