Reasons for drops in alignment

Hello,

I have a set of sequences for a group of individuals subdivided into normal tissue, cancer, and metastasis samples. The mean read count for the group is 542 350 341, but in three samples the count is zero.

What might be the causes for such a drop in quality?

Thank you

alignment quality

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updated 5.4 years ago by German.M.Demidov

• written 5.4 years ago by marongiu.luigi

I would say that if your read count is 0, BAM file is corrupted or your pipeline failed at some stage in these samples.

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written 5.4 years ago by German.M.Demidov

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