How to run faToTwoBit on the FASTA format sequence?

Question

[sabreenaalam12345]

Hello, I am trying to convert the FASTA sequence in to two-bit format by faToTwoBit program downloaded from UCSC genome browser. I have converted it to executable bit but am unable to run the program on my FASTA sequence. What is the command line to run it?Please help.

Answer 1

[GenoMax]

If you run the program on its own without any options it will show you how to use it

$ ./faToTwoBit 
faToTwoBit - Convert DNA from fasta to 2bit format
usage:
   faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit

So use one or more input fasta files and provide an output name out.2bit.

[sabreenaalam12345]

I have found this usage but did not understand it, please clarify.

I have put this command faToTwoBit Chr1.fa out.2bit but the terminal shows faToTwoBit: command not found....why is this happening?

[GenoMax]

command not found....why is this happening?

That is because the directory you are in is not part of $PATH.

Use as follows (replace with real names you have/need). Note the period and slash before program name.

$ ./faTwoBit your_file.fa name_for_2bit_file.2bit

[sabreenaalam12345]

I did as you mentioned. I put the command ./faToTwoBit Chr1.fa.2bit This appeared again:

faToTwoBit - Convert DNA from fasta to 2bit format usage: faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit options: -long use 64-bit offsets for index. Allow for twoBit to contain more than 4Gb of sequence. NOT COMPATIBLE WITH OLDER CODE. -noMask Ignore lower-case masking in fa file. -stripVersion Strip off version number after '.' for GenBank accessions. -ignoreDups Convert first sequence only if there are duplicate sequence names. Use 'twoBitDup' to find duplicate sequences.

What is wrong in the command?

[GenoMax]

You need to use

 ./faToTwoBit Chr1.fa Chr1.2bit

Note space separating the two file names.

[sabreenaalam12345]

I have used the command you mentioned, actually nothing happened. It returned to its original $ position again

[GenoMax]

That means the command worked and made the Chr1.2bit file. You can check that by listing the files.

Sounds like you need to get familiar with basic command line skills. Please spend some time on that first. I recommend: https://angus.readthedocs.io/en/2019/shell_intro/index.html

[sabreenaalam12345]

Yes, I am completely new to Linux and still learning. Thank You! It worked. Thanks for the link too.