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  • Mapping ChIP-seq paired end data with bowtie2

    Hi!

    Having some trouble with bowtie2 rn

    Using public data from an encode entry for my course project and can get past this error:

    readU: Success
    (ERR): bowtie2-align exited with value 1​

    Here is my code:

    bowtie2-build chm13v2.0.fa.qz chm13v2_bt2
    bowtie2 -x chm13v2_bt2 -1 ENCFF025YQV.fastq.gz -2 ENCFF572GPA.fastq.gz | awk '$2 != 4 {print}' | samtools view -S -b '-' > NUFIP1_CHiPseq_PE_output.bam

    Also tried running simplified version, but some error result:

    bowtie2 -x chm13v2_bt2 -1 ENCFF025YQV.fastq.gz -2 ENCFF572GPA.fastq.gz -S NUFIP1_CHiPseq_PE_output.sam

    Does anyone have any ideas?
    Thank you

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