Hello.
I am trying to use RepeatModeler to identify transposable elements in a genome of C. Remanei. I have a FASTQ file that came from a genome analysis. I'm trying to convert the FASTQ file to a FASTA file with the following format:
> name
ACGCTGCGT..... (sequence)
When I looked around on this site, I saw commands that converts FASTQ to FASTA. However, I used two of such commands and got the same output. For example, the first few lines of my input is:
@NB551191:275:HMT7LBGX7:1:11101:1614:1054 1:N:0:ATCACG
TAAATNAGATCATTTTTGTAGAGAAAAANGANGGCTTNCGAATGGTATGAAAATCTCTGTGATCCGTCAAAAACTGACTGAGTTCTGATAAAAAATGTATTGGCAGAAAATACCACTTGGACCAAATCTCAAAAATTGACGGAAATGTCAC
+
AAAAA#EEEEEEEEEEEEEEEEEAEEEE#EE#EEEEE#EEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE/AAAEEEEEAEEEAA<EEAEEEEAEEEEEEEAAEEEE
@NB551191:275:HMT7LBGX7:1:11101:18472:1054 1:N:0:ATCACG
TTTCCNGAAAACGCATCCAGCATTGTTTNACNTCATTNGAGAGCTGAAAATTTTCAAACCTGTATTTTCCAATCGCATAATAACTCGTGTCTCCTTCTCCATAATCCGTGGGAAGCTTTCAACTCAATAAATTTTAGGAAAAAAGTTTATT
+
AAAAA#EEEE6EEE/AEEEEEEEEEEEE#AE#EEEEE#EEEEEEEEEEEE/EEEAEE/EEEEEEEEEEEAE/EEEAAAEAEEEEEEEE/EEEEEEEEEAEE/EE<<EEEAEEEAEE<<<EA/EEAA</AEEEAAEAEEEA/EEEA/EAEAA
> (ad infinitum)
And when I use the command to convert to FASTA, I get this output:
>NB551191:275:HMT7LBGX7:1:11101:1614:1054 1:N:0:ATCACG
TAAATNAGATCATTTTTGTAGAGAAAAANGANGGCTTNCGAATGGTATGAAAATCTCTGTGATCCGTCAAAAACTGACTGAGTTCTGATAAAAAATGTATTGGCAGAAAATACCACTTGGACCAAATCTCAAAAATTGACGGAAATGTCAC
>NB551191:275:HMT7LBGX7:1:11101:18472:1054 1:N:0:ATCACG
TTTCCNGAAAACGCATCCAGCATTGTTTNACNTCATTNGAGAGCTGAAAATTTTCAAACCTGTATTTTCCAATCGCATAATAACTCGTGTCTCCTTCTCCATAATCCGTGGGAAGCTTTCAACTCAATAAATTTTAGGAAAAAAGTTTATT
> (ad infinitum)
This is not the format I want; I want a FASTA file that only contains 1 description and the rest of the file be the sequence. From a FASTQ file, is it possible to obtain this, and if so how do I do so? If not, how should I run the data through RepeatModeler? Thank you for your help!
1 answer
The procedure you were given does convert a fastq to fasta. So that's not actually what you want to do.
The reads in a fastq are almost certainly unplaced. You can't just string them together in order and get a sequence that makes sense. I think you want a consensus sequence, so you need to look up how to do that. You can either do de novo assembly, or align to a reference, and make a consensus sequence taking in account the points where your reads differ from the consensus.
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Are you sure this is what you need to do?
If so, search is your friend. See, for example: HOw to merge multifasta sequence into a single sequence having only one header?.
You could simply drop all lines that start with
>by piping your file throughgrep -v "^>"and then append a header you want at top.But these would still be individual reads and not represent what the sequence of the genome is. Which I assume you ultimately want to use with repeatmodeler?
Yes you are correct. I want the sequence of the whole genome (as a FASTA file) given a FASTQ file. How can I obtain this?
Unfortunately what you want to do is not correct, the FastQ files represent some data sequencing of your genome, that means that the genome was fragmented in such small sequences. I guess what you want is to first assemble your reads into contigs and use those to predict/detect repetitive elements.
Ah that makes sense. Is there some sort of tool to assembly contigs from FASTQ files? I'm also moderately proficient in Python and Java if there's some simple lines of code that I can write to do this.
No. Do not reinvent the wheel. Google for programs that will do what you want. You can likely find answers on biostars that are relevant.