Question: ChIP-Sequencing data analysis
gravatar for umadaan
3.1 years ago by
United States
umadaan0 wrote:


I am trying to analyze ChIP-Seq data and extract enriched motifs from it. I have done the tabular to fasta conversions and sorted it based on length, I have also done the genomic features extraction. However, when I try to generate logo plots, either I get a message saying the lengths are not equal or the logo plots that are generated are completely empty. I am not quite sure what I am doing wrong at this point. Any help will be greatly appreciated. Is there a way to make the sequences all the same length? Thank you.




chip logoplot motif galaxy • 727 views
ADD COMMENTlink modified 3.1 years ago by Jennifer Hillman Jackson25k • written 3.1 years ago by umadaan0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Has the data been through the tool ClustalW? That is a precursor step for the tool Sequence Logo.

The fasta sequences must be all the same length. Sequences can be trimmed if needed (not Illumina) or maybe the originals (if Illumina) should not be trimmed or all trimmed to a consistent length prior to executing ClustalW? Tools for trimming are in the group Fastq manipulation.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson25k
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