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Question: HiSat2- over 50% of reads failed to align
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gravatar for Lindsay44
2.4 years ago by
Lindsay44 • 0
Lindsay44 • 0 wrote:

Hello,

I am using Hisat2 to align reads to a reference genome (mm10).

However, over 50% of reads failed to align to the genome.

What went wrong? Is it the reference genome I am using? Is it the quality of the data?

Thanks.
rna-seq alignment • 2.0k views
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modified 2.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.4 years ago by Lindsay44 • 0
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gravatar for Jennifer Hillman Jackson
2.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It could be due to any of these reasons: the setting used with the tool, the fastq sequence quality score scaling, the format of a custom reference genome (if used), the quality of the custom reference genome assembly (again, if used), the quality of the sequence reads (run FastQC after confirming quality score scaling to check and QA as needed).

Help links:

Best, Jen, Galaxy team
ADD COMMENT • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k
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