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  • how can I align 10 fastq files and get the htseq-count on Mac

    Hello,

    I have been strugelling to run Hisat2 code for alignment of several fastq files from human
    I have read as many post as I could online and I went through the protocol here


    At the moment, i have the latest binary version of hisat2 in $HOME/bin
    When I do hisat2 in the terminal and is shows that I don't import any input but it indicates that it is there and can be invoked

    No index, query, or output file specified!
    HISAT2 version 2.1.0 by Daehwan Kim ([email protected], www.ccb.jhu.edu/people/infphilo)
    Usage:


    I have 10 fasta files on a folder named data on my desktop.
    I have put the three scripts attached to the protocl in that folder and the files are shown below

    NIHMS816842-supplement-README.txt
    RNAseq_shell_script.sh
    SRR1_1.fastq.gz SRR9_1.fastq.gz
    SRR1_2.fastq.gz SRR9_2.fastq.gz
    SRR2_1.fastq.gz SRR10_1.fastq.gz
    SRR2_2.fastq.gz SRR10_2.fastq.gz
    SRR3_1.fastq.gz
    SRR3_2.fastq.gz
    SRR4_1.fastq.gz
    SRR4_2.fastq.gz
    SRR5_1.fastq.gz
    SRR5_2.fastq.gz
    SRR6_1.fastq.gz
    SRR6_2.fastq.gz
    SRR7_1.fastq.gz
    SRR7_2.fastq.gz rnaseq_ballgown.R
    SRR8_1.fastq.gz rnaseq_pipeline.config.sh
    SRR8_2.fastq.gz


    Can you please let me know how I can run your code to align these fastq files with a Human gene reference ?

    I did not change anything on any of the script which I believe that I must change the one in rnaseq_pipline.config.sh

    At this moment, it is

    NUMCPUS=8
    HISAT2=$(which hisat2)
    STRINGTIE=$(which stringtie)
    SAMTOOLS=$(which samtools)
    BASEDIR=$(pwd -P)/chrX_data
    FASTQLOC="$BASEDIR/samples"
    GENOMEIDX="$BASEDIR/indexes/chrX_tran"
    GTFFILE="$BASEDIR/genes/chrX.gtf"
    PHENODATA="$BASEDIR/geuvadis_phenodata.csv"
    TEMPLOC="./tmp" #this will be relative to the output directory
    reads1=(${FASTQLOC}/*_1.*)
    reads1=("${reads1[@]##*/}")
    reads2=("${reads1[@]/_1./_2.}")


    All what I want is to get the htseq-count. txt files for each sample

    I am looking forward to hearing from you
    Best Regards,
    Nik

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