Question: FIMO output that preserves padj values
gravatar for rbronste
17 months ago by
rbronste340 wrote:

Hi I am generating a fasta file from a DESeq2 output in the following way:

bedtools getfasta -fi /son/genomes/mm10.fa -bed treatment_pw_padj.001_sorted.bed -fo treatment_pw_padj.001_sorted.fa

The above bed file has FDR information as a last column, I believe #12

I then run the following to search for instances of a specific motifs within these intervals:

fimo /son/ /son/treatment_pw_padj.001_sorted.fa

I get a list of located motif sites with p-values however I would like to preserve the DESeq2 FDR value located in the original bed file as well next to these newly filtered intervals, any ideas on how I could do that? Thank you.

motifs chip-seq deseq2 meme fimo • 473 views
ADD COMMENTlink written 17 months ago by rbronste340

Why don't you make a custom fasta header for every entry that contains the column information like:

ADD REPLYlink written 17 months ago by ATpoint29k

I think your method is much better.

ADD REPLYlink modified 17 months ago • written 17 months ago by morovatunc400

I like to keep things silmpe whenever I can ;-D

ADD REPLYlink written 17 months ago by ATpoint29k

What would be your preferred method of making the custom fasta header and is this something I can output from bedtools getfasta, so it maintains a column from the initial bed file Im making into a fasta? Thanks!

ADD REPLYlink written 17 months ago by rbronste340

I dont have your data at the moment therefore I cannot give explicit solution but I can show you the way

R has a function called We are gonna use this to merge your initial data with the latest fimo output. So In the end you will have BED + fimo merged together. (probably, you will have duplicated rows of that BED since fimo might find multiple motifs in the single binding region)

1) So use bedtools getfasta with -name option on it. Then run fimo.

2) In fimo's txt output, there should be sequence name column. Extract your that peak name as they will become identical as write-in your input bed.

3) then use function(in R base) to merge those two and get a single data frame.

4) make proper filtration to remove unnecessary data. (well you can make this step after reading your files as well)

If you can send me a sample, I can code it as well.

ADD REPLYlink modified 17 months ago • written 17 months ago by morovatunc400
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