Question about strand-specificity of transcript alignment

[Nina G]

Hello everyone,

I am searching for non-synonymous SNPs leading to amino acid substitutions using aligned mRNA-seq data. I faced one problem: some genes on -1 strand are aligned to genome as belonging to +1 strand. In other words, IGV indicates SNP although the nucleotide in the transcript is the same as in the reference, when the strand is oriented in a proper way (screenshot is attached). When I change the strand direction to +1, SNP looks logic, but the gene should be in -1 orientation. What could be a problem? incorrect mapping or something else? We made RNAseq using 100bp paired-end strategy, without strand-specificity.

Best regards,

NIna Gubina.

[Jim Robinson]

Hi,

There isn't really a problem here, everything looks normal.   The arrow to the left of the sequence is not indicating the strand of the gene, for that you need to look at the gene annotation track.  You could in fact have overlapping genes on opposite strands at any given location.   The arrow is just showing for which strand sequence is displayed.   "Flipping" it just complements the strand.  

So everything in your picture looks correct, there is indeed a snp at the location shown.  There is no problem with your library or mapping (at least no problem visible from this picture).  

Jim

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[Nina G]

Hi Jim,

Thank you for the reply!

Best regards,

Nina.

четверг, 4 декабря 2014 г., 16:49:50 UTC+3 пользователь Jim Robinson написал: