Obtain number of base pairs in a genome

Question

[Nika]

HI!

It's going to be a stupid question since I'm not anyhow related to bioinformatics - I'm interested into how can I obtain the number of base pairs in my genome sample. I'm trying to remake the experiment that was made in an article - and since the authors are not responsive, I'm posting my question here. The authors stated they only picked samples with at least 1 billion bases for further analysis. I downloaded the data from ENA repository, got a bunch of files - the data is metagenome data. I checked the quality with FastQC and mapped them to GRCh37 - the authors used it as a reference genome. Now I'm trying to figure out how to obtain the number of base pairs for my sample? Is it stated somewhere in FastQC reports or can I obtain it using IGV or some other tool? I'm lost at this point.

Thank you for your help.

BR,
Nika

p.s.: if my post is not according to the guidance for posts, I'm really sorry. It's because when I click on Posting Guide under See Posting Guide for guidance on creating a post it just returns to homepage stating the post doesn't exist anymore.

Answer 1

[GenoMax]

Probably other ways of doing this but you could use BBTools and the program below.

  $ reformat.sh -Xmx4g in=your_fastq.gz

You will see something like following in summary message

Input:                          34448 reads             8612000 bases
Output:                         34448 reads (100.00%)   8612000 bases (100.00%)

This tells you the number of reads in the file and total base count.

You can also use this on a multi-fasta genome file (tells you there are 26 fasta sequences in file)

$ reformat.sh -Xmx4g in=genome.fa

Input:                          26 reads                1340447187 bases
Output:                         26 reads (100.00%)      1340447187 bases (100.00%)

[Nika]

Thank you so much for your reply! I tried it and it works - thanks a lot, that's just what I needed!