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Old 10-31-2013, 09:28 AM   #4
Location: DC area

Join Date: Sep 2011
Posts: 42

Hello all,
I have a similar related question to extract chromosome positions and depth per region. So I used bedtools to get bam to bed conversion:
I got :
Chr1 11419 11425 HWUSI-# 1 + 1
Chr1 13877 13892 HWUSI-# 0 - 2
Chr1 14714 14721 HWUSI-# 1 + 3
Chr1 16155 16163 HWUSI-# 1 - 4
Chr1 18239 18249 HWUSI-# 1 + 5
Now I looked up the manual for bedtools and it indicates that col5 as scores 1 to 1000 . I tried looking more into it, but cannot understand what those 1 and 0s stand for specifically.I know they are scores and that's it. I also have downstream in this column 32, 42 etc and not jut 1 or 0.I have cut and pasted just the top 5 outputs.
Also the last column looks like it is assigned a number for each cluster. Is this correct?
Please can some one clarify this for me?
Also if I need to get just the first 4 columns as is and also get the seq itself in the next column and counts of tags in the next columns, can I use bedtools to do it? If so , how? or do I need to write a script so that I have:
Chr# start end name seq # of tags pos/neg strand cluster#. from my bam files?
Please any help will do
Thanks in advance
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