Some questions about the input format

[biozzq]

Dear all,

I usually convert the allValidPairs to the input file for juicer by using hicpro2juicebox.sh. However, when I learn how the shell script works (the following command), I found that I didn't remove the "chr" substring in chromosomes in my previous analysis. And more, do we need to rearrange the record for each read pair, such as the first read precedes the chromosome of the second read ($2 <= $5) when they are on different chromosomes; the first read precedes the position in base pairs of the second read when the read pair share the same chromosome? Thank you.

awk '{$4=$4!="+"; $7=$7!="+"} $2<=$5{print $1, $4, $2, $3, 0, $7, $5, $6, 1, $11, $12 }$5<$2{ print $1, $7, $5, $6, 0, $4, $2, $3, 1, $12, $11 }' $VALIDPAIRS | sort -T ${TEMP} -k3,3d -k7,7d -S 50% --parallel=8 > ${TEMP}/$$_allValidPairs.pre_juicebox_sorted

Sincerely, Zheng zhuqing

[nchernia]

You don't need to remove the "chr" if it was present in your fasta.

And yes you need to rearrange. This script looks fine.

On Wed, Mar 31, 2021 at 12:36 AM biozzq @.***> wrote:

Dear all,

I usually convert the allValidPairs to the input file for juicer by using hicpro2juicebox.sh. However, when I learn how the shell script works (the following command), I found that I didn't remove the "chr" substring in chromosomes in my previous analysis. And more, do we need to rearrange the record for each read pair, such as the first read precedes the chromosome of the second read ($2 <= $5) when they are on different chromosomes; the first read precedes the position in base pairs of the second read when the read pair share the same chromosome? Thank you.

awk '{$4=$4!="+"; $7=$7!="+"} $2<=$5{print $1, $4, $2, $3, 0, $7, $5, $6, 1, $11, $12 }$5<$2{ print $1, $7, $5, $6, 0, $4, $2, $3, 1, $12, $11 }' $VALIDPAIRS | sort -T ${TEMP} -k3,3d -k7,7d -S 50% --parallel=8 > ${TEMP}/$$_allValidPairs.pre_juicebox_sorted

Sincerely, Zheng zhuqing

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[biozzq]

Dear @nchernia

Thank you.

Best,