Question: Is there a way to choose only exon annotations from an annotated peak .txt file to generate a metagene analysis?
0
gravatar for System
4.7 years ago by
System170
United States
System170 wrote:

A lab member recently ran a ChIP-Seq on Pol-II and gave me the files from sequencing to annotate. I generated a annotated peak file in the following format:

 
PeakID
Chr
Start
End
Strand
Peak Score
Focus Ratio/Region Size
Annotation
Detailed Annotation
Distance to TSS
Nearest PromoterID
Entrez ID
Nearest Unigene
Nearest Refseq
Nearest Ensembl
Gene Name
Gene Alias
Gene Description
Gene Type
Pol-II-Chip.MACS2_peak_77166
chr6
74229770
74231637
+
7081
NA
promoter-TSS (EEF1A1)
promoter-TSS (NM_001402)
52
EEF1A1
1915
Hs.745122
XM_005248666
ENSG00000156508
EEF1A1
CCS-3|CCS3|EE1A1|EEF-1|EEF1A|EF-Tu|EF1A|GRAF-1EF|HNGC:16303|LENG7|PTI1|eEF1A-1
eukaryotic translation elongation factor 1 alpha 1
protein-coding

However he wants to generate a metagene graph of only the exon regions. I attempted to simply sort and remove all the rows that were not exons, but my python script was unable to detect peakfile formatted lines when I did this. Is there a way to choose only exon annotations from a txt file like this? I've realized any sort of sorting done in excel will throw my script off and not allow it to read peak file formatted lines. 

 

If this isn't possible, how could I get only exon annotations from a .narrowPeak file?

peak file excel chip-seq • 1.6k views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by System170

Could you clarify a little, for example by stating the hypothesis to test, such as "Pol II will be enriched at the start of each exon" vs "Pol-II will be enriched in exons vs introns", etc. I think I could help a bit if you made your goals clearer.

ADD REPLYlink written 4.7 years ago by Joseph Pearson450
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