input file for "pre" command

[Shuang-Yin Wang]

Hi,

I have generated paired contacts of reads using my own pipeline. Now, I am trying out the juicer package.

I have some questions about the 11 columns file, 

1. Do I need to provide readname?

2. Is the "pos" 5' end of the read end or the pos in the bam file from bwa?

3. I have "frag" information, but it is based on my own index. How can I check whether they are consistent with the indexing in juicer?

Best regards,

Shuang-Yin

[Neva Durand]

Hello Shuang-Yin,

1. Do I need to provide readname?

You should have something in the first column but it can be a fake readname; it is ignored by the software.

 

2. Is the "pos" 5' end of the read end or the pos in the bam file from bwa?

It's the 5' end of the read end.

 

3. I have "frag" information, but it is based on my own index. How can I check whether they are consistent with the indexing in juicer?

The Python script linked below generates the site positions from the fasta file, and the Perl script assigns fragments from an intermediate file.  You could spot check your reads against what these would return.

https://github.com/theaidenlab/juicer/blob/master/misc/generate_site_positions.py

https://github.com/theaidenlab/juicer/blob/master/UGER/scripts/fragment.pl

Best

Neva

 

Best regards,

Shuang-Yin

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org