How to prepare bed files needed by motif finder?

[Aoi Summer]

Hi,

   I'm trying to analysis zebrafish HiC data by Juicer, and was stuck running motif finder. I used FIMO to creat a CTCF bed file from zebrafish genome. But have no idea how to prepare files needed in unique and inferred folder. Is there any suggestion? I just want to annotate CTCF locations for the hic files.

Best

Aoi

[Neva Durand]

Hello,

Please have a look at the documentation here:

https://github.com/theaidenlab/juicer/wiki/MotifFinder

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

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[Aoi Summer]

I used ctcf bed file from chip-seq data, but the output looked like this: 

Skipping >1 dna:chromosome chromosome:GRCz10:1:1:58871917:1 REF

Skipping GATCTTAAACATTTATTCCCCCTGCAAACATTTTCAATCATTACATTGTCATTTCCCCTC

Skipping CAAATTAAATTTAGCCAGAGGCGCACAACATACGACCTCTAAAAAAGGTGCTGTAACATG

Skipping TACCTATATGCAGCACCACTATATGAGAGCGGCATAGCAGTGTTTAGTCACTTGGTTGCT

...

Unable to find proper file via VIA_ID

motifs <genomeID> <bed_file_dir> <looplist> [custom_global_motif_list]

I putted bowtie index here for <genomeID> but I saw the warning messages without this option just announced that it needs chromosomal size file

Could not find chromosome sizes file for: zebrafish

So what kind of files should I prepare? 

On Tuesday, September 12, 2017 at 11:31:25 PM UTC+8, Neva Durand wrote:

Hello,

Please have a look at the documentation here:

https://github.com/theaidenlab/juicer/wiki/MotifFinder

Best

Neva

On Thu, Sep 7, 2017 at 10:38 PM, Aoi Summer <stca...@gmail.com> wrote:

Hi,

   I'm trying to analysis zebrafish HiC data by Juicer, and was stuck running motif finder. I used FIMO to creat a CTCF bed file from zebrafish genome. But have no idea how to prepare files needed in unique and inferred folder. Is there any suggestion? I just want to annotate CTCF locations for the hic files.

Best

Aoi

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[Neva Durand]

The chrom.sizes file is from UCSC; it is tab separated and for each line, has the chromosome name followed by the size of the file.  If your genomeID is not one already in Juicer tools (which it is not) you should get that file from UCSC or create it yourself and use that for the <genome_id> field.

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