Question: (Closed) what does this formula represent?
0
gravatar for AAK85
2.9 years ago by
AAK850
AAK850 wrote:

Hi All I was wondering if anyone can help me with the answer of this formula:

[(number of bases in an interval * number of primary alignments)/ number of reads in an interval] *1e9

[number of bases in an interval * total number of reads)/ number of reads in an interval] * 1e9

I have the $7 and $8 column representing the starting point and ending point of an interval. I have the number of primary alignmets through this command: samtools view -F 0x100 A.bam | awk 'END {printf NR " "}' I have number of reads in an interval by this command : samtoold view -F 0X100 A.bam " chr1:10000-10468" | wc -l Now I want to know what do we get using these data in the formula and what the result of the formula represent? Thank you.

sequencing genome • 689 views
ADD COMMENTlink modified 2.9 years ago by Michael Dondrup47k • written 2.9 years ago by AAK850

Hello aida.ansari85!

We believe that this post does not fit the main topic of this site.

Please don't post the same question in a new thread: repeatmasker file analysis
Since you have partially worked your way through the answer, why not go through all the way.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by genomax80k

Hi The topic of the site I thought is helping people to analyze the genome data. I have a command that I cannot undestand why we divide the number of bases of the interval multyplied by the total number of alignmets to number of reads within an interval? This can be a very simple question for the experts but as I'm new to this field I needed some help to understand the command and the result of it. If anyone can help I'll appreciate it. Regards Aida

ADD REPLYlink written 2.9 years ago by AAK850

AAK85 : Can you provide full context of what you are trying to do? You can't post a command from a larger workflow and expect folks to understand the full context.

You also need to specify (and/or provide examples) examples of inputs and outputs for the command. It sounds like for both questions you had posted you are able to get something but can't understand what the output means?

We are fully willing to help, we just want to get a clear description of the question. Please take a look at this for guidance: How To Ask Good Questions On Technical And Scientific Forums

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by genomax80k

It doesn't look like an identical question to me at first glance, it is hard to understand without the context though. Looks a bit like trying to calculate RPKM? Anyway, it is unclear what

Now I want to know what do we get using these data in the formula and what the result of the formula represent?

means, when we don't know where the formula comes from.

ADD REPLYlink written 2.9 years ago by Michael Dondrup47k

Hi Thank you so much for your reply. Yes, I checked with my colleague, this is calculating RPKM. Thanks alot again.

ADD REPLYlink written 2.9 years ago by AAK850
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