Question: HiSat2- over 50% of reads failed to align
0
gravatar for Lindsay44
22 months ago by
Lindsay440
Lindsay440 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 • 1.4k views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson24k • written 22 months ago by Lindsay440
0
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson24k 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 COMMENTlink written 22 months ago by Jennifer Hillman Jackson24k
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