Hello everyone,
Has anyone used abpair function in maq_plot.pl? I just run into a problem of using it. Abpair is a function that designed to plot the abnormal pair reads along the chromosome, by inputting the information such as chromosome, start position and end position for the paired-end reads and orientation for two reads (indicate if they are FF FR RF or RR). The command is like:
maq_plot.pl abpair [-m 250] [-M 1000000] [-c chr] <prefix> <abpair-output>
-m -M are the distance to filter the paired-end reads with abnormal distance
My problem is about <abpair-output> file. It should be a tab delimited input file to plot the figure.
However, I did not find how to generate the abpair-output. It should be generated by other command in MAC, but I just could not find the right way to do it. Anyone has a suggestion?
Thank you in advance!
Yu
Has anyone used abpair function in maq_plot.pl? I just run into a problem of using it. Abpair is a function that designed to plot the abnormal pair reads along the chromosome, by inputting the information such as chromosome, start position and end position for the paired-end reads and orientation for two reads (indicate if they are FF FR RF or RR). The command is like:
maq_plot.pl abpair [-m 250] [-M 1000000] [-c chr] <prefix> <abpair-output>
-m -M are the distance to filter the paired-end reads with abnormal distance
My problem is about <abpair-output> file. It should be a tab delimited input file to plot the figure.
However, I did not find how to generate the abpair-output. It should be generated by other command in MAC, but I just could not find the right way to do it. Anyone has a suggestion?
Thank you in advance!
Yu
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