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missing coordinates in raw data but seeing peaks in IGB

Hello,

I am very new to ChIP-Sequence Analysis. I received some data and first looked at the raw coordinates for chromosome for genes of interest. One gene of interest did not seem to be a target for binding because the coordinates for that gene were not listed in the raw data. However, when I look at that gene using IGB and using a normalized file, I see very strong peaks in and around that gene. Is there some thing that I might be doing wrong? Thank you.

Best,
Uday

chip-seq
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updated by Ram 4.5K • | written by uday20030 0
  1. How are you checking the files other than IGB (I presume something like samtools view)?
  2. What do you see if you look at the non-normalized files in IGB?
  3. Are you sure you're looking at the same place in IGB and elsewhere?
• 0 views • link
updated by Ram 4.5K • | written by Devon Ryan 10K

Hi Devon,

Thank you for the reply

  1. The files with coordinates are all in excel format, hence I can just match the coordinates with the coordinates of the gene of interest.
  2. I actually never looked at the non-normalized files.
  3. I am definitely sure I am looking at the right place in the genome.

I can look at the non-normalized file and get back to you asap.

Best,
Uday

• 0 views • link
updated by Ram 4.5K • | written by uday20030 0

Hopefully the non-normalized files are informative. If not I haven't a clue :(

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updated by Ram 4.5K • | written by Devon Ryan 10K

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