what is the reason of fastqc software different in QC% in fastq1 fastq2

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12 months ago

wdpang • 0

Hi,

if have microbial contamination from the two peak of QC%, why is different of fastq1 and fastq2 picutre?

fq1 enter image description here

fq2 enter image description here

QC fastqc • 648 views

ADD COMMENT • link 12 months ago by wdpang • 0

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We won't be able to help unless you provide detailed information on what you're doing.

ADD REPLY • link 12 months ago by rpolicastro 13k

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Hi,

The data is RNA-seq clean data from human cfRNA non specific library which use fastp to filter low quality reads and ployA,T. And then use fastqc to quality control.

supplement, The alinment result of STAR and HISTAT2. The bad mapping result is a question .The result is following:

enter image description here

Due to the low mapping rate, i use the kraken2 to class the unmap reads which use the 300G library. Only 40% reads can class. The result is following:

enter image description here

i would appreciate if you could give me some advice.

ADD REPLY • link 12 months ago by wdpang • 0

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