Question: (Closed) what does this formula represent?

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AAK85 •

**0**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.

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modified 2.9 years ago
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Michael Dondrup ♦

**47k**• written 2.9 years ago by AAK85 •**0**
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!

80kHi 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

0AAK85 : 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

80kIt 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

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

47kHi Thank you so much for your reply. Yes, I checked with my colleague, this is calculating RPKM. Thanks alot again.

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