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Old 07-05-2015, 02:53 PM   #7
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Location: Denver, CO

Join Date: May 2015
Posts: 6

I do primarily single ended reads, but for alignment quality I look primarily at
1) pct of reads mapped
2) pct of reads uniquely mapped

It sounds like you are also asking about post-alignment qc in general and I add
3) read duplication (ie how many reads align to identical location) - most reads should have only one or several.
4) reads biotype distribution (most should map to protein-coding regions)
5) cumulative pct measures - I sort genes by count or fpkm and graph # of genes vs cumulative percentage. That will tell you if you are sinking a lot of reads into very common transcripts and tell you that you might need more depth to see certain less common transcripts.
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