HiCorr/bin/preprocess/pairing_two_SAM_reads.pl: No such file or directory

[PhilicJone]

I meet some errors when runing documents/DPNII_preprocessing.sh
Here is the error：
XXX/HiCorr/bin/preprocess/pairing_two_SAM_reads.pl: No such file or directory
XXX/HiCorr/bin/preprocess/remove_dup_PE_SAM_sorted.pl: No such file or directory

Besides, I am not clear about the “$” in front of “bowtie”, I deleted them when I ran it, do you think it is right

1. mapping, take 50bp for mapping

cat $fq1 | $lib/reformat_fastq.py 1 50 | $bowtie -v 3 -m 1 --best --strata --time -p 10 --sam $hg19 - > $name.R1.sam &
cat $fq2 | $lib/reformat_fastq.py 1 50 | $bowtie -v 3 -m 1 --best --strata --time -p 10 --sam $hg19 - > $name.R2.sam &

[YitingLi6]

You have already set the path corresponding to bowtie=it in the front, and adding $ refers to the path you set, and it must not be deleted. If you still can't solve it, let's switch to the absolute path.