thank you, it worked !
• 0 views
•
link
written
by
giroudpaul
[Resolved] Help in Data management : regrouping result
Hello !
I am trying to have a file that concatenate the output from Fimo with the ones from Homer annotatePeaks. In the end, I want to have one big tab separated file with the peak data, the sequence that matched my consensus motif and then homer annotation.
This is my fimo output (note, I also have it with chr/start/end position; but I can't have both on the same file)
#name strand score p-value q-valut match_seq
MACS_peak_625 - 25.5902 1.93e-09 0.00498 GAGTTCACCGAGTTCA
MACS_peak_4881 + 25.4426 2.41e-09 0.00498 GAGTTCACTGAGTTCA
MACS_peak_16939 + 25.0984 3.08e-09 0.00498 GAGTTCATAGAGTTCA
MACS_peak_6882 - 25.0984 3.08e-09 0.00498 GAGTTCATAGAGTTCA
MACS_peak_4617 - 25.0984 3.08e-09 0.00498 GAGTTCATAGAGTTCA
MACS_peak_6695 + 25.0164 3.51e-09 0.00498 GAGTTCACTGGGTTCA
MACS_peak_14937 + 24.5902 4.36e-09 0.00514 GGGTTCACTGGGTTCA
MACS_peak_16708 + 24.2295 4.84e-09 0.00514 GAGTTCACAGAGTTCA
And this is my annotation file of my .bed
PeakID Chr Start End Strand Peak Score Rest_of_annotation_columns
MACS_peak_9638 chr17 39985383 39985583 + 529.00 ...
Is there a way to "grep" and concatenate both files so that I have:
MACS_peak_X chrX start end strand score(frombed) match_seq score(fromfimo) p-value q-value rest_of_homer_annotation...
• 2,205 views
•
link
updated
by
Ram
•
written
by
giroudpaul
•
written
by
giroudpaul
1 answer
Disclaimer: Column headers are going to get messed up in this solution (or you could remove them beforehand and then run the command).
$ join <( sort fimo_output) <(sort bed_file) | tac | awk '{print $1,$7,$8,$9,$11,$6,$3,$4,$5}' | column -t
Field numbers in the awk part will have to be changed based on how many additional columns you have in your bed file. You should be able to figure that part out.
Based on a solution here.
Log in to answer this question.