how many sequences are in genome file

Question

[ikramb450]

how can we check that,the how many sequences are in genome file...?

[Pierre Lindenbaum]

please define "genome file"

also: what did you try ?

[ikramb450]

i want to extract the only sequences counting in genome file...

[ATpoint]

What is a genome file, and please don't use the term 'genome file' in the comment to that.

[ikramb450]

genome file means gtf file which is fasta file

[swbarnes2]

A gtf is not a fasta file.

[ikramb450]

ok...but in my question which is asking me by my teacher he says to me that the how many sequences are in genome file.... and which file provided me by my teachers which is *.gtf file so thats why is just call it.....

[ikramb450]

but now i am totally confused .... that how can i get sequence from a file..?

[ATpoint]

This is a pointless discussion. You apparently do not know what you are working with so either provide a snippet if the file here or ask the person who gave it for details.

[ikramb450]

sorry for disturbance but its not my motive i am beginner so i have not a wide knowledge about unix and my research is all about on the bioinformatics so thats why i just try to get some knowledge from this site and thats why i previously demanding a youtube channel through which i can learn about unix commands and how can we do work on it.... once again sorry i hope you understand my situation

[4galaxy77]

Rather than apologising (no need for that), actually read what people are saying to you and provide a sample of the file you’ve been given. Try and make it easy for people to help you rather than guessing, or else you’ll find that nobody will help. Please also show a bit of evidence that you’ve tried to solve this question yourself rather than dumping it here.

I have a lot of sympathy - I remember being a beginner and not knowing much (see the awful early posts I made here). It’s very hard as bioinformatics is a jungle at times. But learning how to seek help and find something out for yourself is the most important skill you’ll learn.

[ikramb450]

now please tell me how can i extracted the counting of sequenes in a file....

[seidel]

...my question which is asking me by my teacher...

Why don't you approach your teacher for guidance? I'm sure they can point you to the resources they are expecting you to learn from.

Answer 1

[rpolicastro]

Assuming you are talking about a fasta file, you can just count the number of lines that start with a right angle bracket >.

grep -c "^>" file.fasta

[ikramb450]

thank you so much can i use also pipe and wc -l for the counting of exect sequnces counting in genome file..?and tgere no samtools is to be used here yes or no..?

[Friederike]

Do you actually have access to the file? If yes, the first step you need to do is to understand what the content of the file looks like. This can be achieved, for example, via head genomefile. You can copy and paste the output here and then we can walk you through the next step. Or you could come up with it yourself and, for example, try whether wc -l will do the trick.