How to get differentially expressed gene sequences (by ids) from Trinity.fasta file.

[clo...@csumb.edu]

Hello,

I am trying to use grep and awk to extract a subset of DE genes from my Trinity.fasta file. I have this, but it only prints the first line of the sequence. How do I modify to include the entire sequence? Is there a way to do this in Trinity?

>head infile
comp1
comp2
comp3
...

head Trinity.fasta

>comp1
ACTCCCTT
>comp2
ACACTGGGT
>compN


cat infile | awk '{print $1}' | grep -A1 -f - Trinity.fasta > good.genes.fa

Thank you!
Cheryl

[Will Holtz]

Consider converting your fasta file to a tabular format with something like fasta_formatter from http://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fhannonlab.cshl.edu%2Ffastx_toolkit%2F. Then do your grepping on the tabular file, and convert back to fasta afterwards if needed.

-Will

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[Dan Browne]

Hi Cheryl,

I wrote a script the other day to do exactly this. It is attached. In order to run it, you will need Python 2.7 and pyfaidx (https://github.com/mdshw5/pyfaidx). Easiest way to install pyfaidx is with pip.

The script takes a list of gene identifiers (TR#|c#_g#) and writes the sequences of all the isoforms (TR#|c#_g#_i#) to a fasta file.

Usage is:

$ python extract_unigene_isoforms -q gene_list.txt -f Trinity_assembly.fa -o output_file.fa

Let me know if you have any questions!

Dan

[Dan Browne]

A note - if you want specific isoforms, not just all isoforms for a given gene - provide a list of the desired isoforms (TR#|c#_g#_i#). Should still work.

[Cheryl Logan]

This solution worked great. I converted my Trinity.fasta file to tabular format using fasta_formatter from the FASTX-Toolkit. 

fasta_formatter -i Trinity.fasta -o Trinity.txt -t

I just had to make one modification to the grep command, so that it prints only 1 line:

cat infile | awk '{print $1}' | grep -A0 -f - Trinity.txt > good.genes.fa

Many Thanks,

Cheryl

[John Craft]

Cheryl

I cannot get your command to work. I have a file with the DE gene list extracted from Trinity_genes.counts.matrix.FCF_vs_FEF.edgeR.DE_results and used it to create a txt file. I have replaced the pipe symbol (|) in the entries of this file and produced Trinity_FCF_FEF_DEgenes_mod1.txt to avoid any character misidentification. I have run Trinity.fasta through fasta_formatter to produce the tabular format and then replaced the pipe in the Trinity.fasta to produce  Trinity_modif4.txt. All of the formats of the files looks OK. I then then ran:

cat Trinity_FCF_FEF_DEgenes_mod1.txt | awk '{print $1}' | grep -A0 -f - Trinity_modif4.txt >Trinity_FCF_FEF_DEgenes_list

but it does not extract any sequences.

I have tested steps along the road and just running

cat Trinity_FCF_FEF_DEgenes_mod1.txt | awk '{print $1}'

produces the DE genes list so I suspect the problem lies in the grep. Running single gene entries with grep -A0 "entry" Trinity_modif4.txt  works fine.

 

Can anyone see where I am going wrong.

Thanks

John

 

 

[Adriana Fróes]

You can use fastacmd script to do that. Just need to format (makeblastdb) you Trinity.fasta and extract the ID genes from the *.subset file (cat file.subset | awk {'print $1'} > outfile.txt).

Adriana M. Froes

Laboratório de Microbiologia, Instituto de Biologia, Depto de Biologia Marinha
Universidade Federal do Rio de Janeiro   
Av. Carlos Chagas Filho 373, Sala A3-202, Bloco A (Anexo) do CCS
21941-599, Ilha do Fundão, Rio de Janeiro, RJ

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[Pavel Eduardo Galindo Torres]

Hi 

This could work 

bioawk -cfastx 'BEGIN{while((getline k <"id_file.txt")>0)i[k]=1}{if(i[$name])print ">"$name, "length="length($seq)"\n"$seq}' Trinity.fasta > final_file.fasta

regards

Pavel 

[Brian Haas]

Lots of ways to do this, of course.

Note, there's a script in the latest Trinity release:

  trinityrnaseq/util/misc/acc_list_to_fasta_entries.pl  

       usage: acc_list_to_fasta_entries.pl   acc.list.txt    file.fasta

that'll extract the list of transcripts from a fasta file based on a list of accessions.

best,

~b

[hex...@gmail.com]

Hi Brian,

Is it possible to use acc_list_to_fasta_entries.pl to extract isoform (or gene) sequences from trinity.fasta for differentially expressed genes? I tried acc_list_to_fasta_entries.pl, and it did not work.

I get list of DE genes (e.g. TR#|c#_g#), and the names of sequences in trinity.fasta are TR#|c#_g#_i#.Dan Browne provided a way to do that, but I have problem to install pyfaidx in the server I use.

Thanks

在 2016年4月20日星期三 UTC-4下午7:11:50，Brian Haas写道：

[Mark Chapman]

Are you trying to extract gene sequences from the trinity.fasta? Genes don't exist they are a combination of expression values from the transcripts. All that's in the fasta file will be transcript sequences.
Best wishes, Mark

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[hex...@gmail.com]

Is it possible to extract all transcripts of selected genes?

在 2016年9月28日星期三 UTC-4下午4:59:31，Mark Chapman写道：

Are you trying to extract gene sequences from the trinity.fasta? Genes don't exist they are a combination of expression values from the transcripts. All that's in the fasta file will be transcript sequences.
Best wishes, Mark

On 28 Sep 2016 19:56, <hex...@gmail.com> wrote:

Hi Brian,

Is it possible to use acc_list_to_fasta_entries.pl to extract isoform (or gene) sequences from trinity.fasta for differentially expressed genes? I tried acc_list_to_fasta_entries.pl, and it did not work.

I get list of DE genes (e.g. TR#|c#_g#), and the names of sequences in trinity.fasta are TR#|c#_g#_i#.Dan Browne provided a way to do that, but I have problem to install pyfaidx in the server I use.

Thanks

在 2016年4月20日星期三 UTC-4下午7:11:50，Brian Haas写道：

Lots of ways to do this, of course.

Note, there's a script in the latest Trinity release:

  trinityrnaseq/util/misc/acc_list_to_fasta_entries.pl  

       usage: acc_list_to_fasta_entries.pl   acc.list.txt    file.fasta

that'll extract the list of transcripts from a fasta file based on a list of accessions.

best,

~b

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[Brian Haas]

Attached is a version of the script that should work for either lists of Trinity genes or list of transcripts.

It'll go in the upcoming release.

best,

~brian

On Wed, Sep 28, 2016 at 7:38 PM, <hex...@gmail.com> wrote:

Is it possible to extract all transcripts of selected genes?

在 2016年9月28日星期三 UTC-4下午4:59:31，Mark Chapman写道：

Are you trying to extract gene sequences from the trinity.fasta? Genes don't exist they are a combination of expression values from the transcripts. All that's in the fasta file will be transcript sequences.
Best wishes, Mark

On 28 Sep 2016 19:56, <hex...@gmail.com> wrote:

Hi Brian,

Is it possible to use acc_list_to_fasta_entries.pl to extract isoform (or gene) sequences from trinity.fasta for differentially expressed genes? I tried acc_list_to_fasta_entries.pl, and it did not work.

I get list of DE genes (e.g. TR#|c#_g#), and the names of sequences in trinity.fasta are TR#|c#_g#_i#.Dan Browne provided a way to do that, but I have problem to install pyfaidx in the server I use.

Thanks

在 2016年4月20日星期三 UTC-4下午7:11:50，Brian Haas写道：

Lots of ways to do this, of course.

Note, there's a script in the latest Trinity release:

  trinityrnaseq/util/misc/acc_list_to_fasta_entries.pl  

       usage: acc_list_to_fasta_entries.pl   acc.list.txt    file.fasta

that'll extract the list of transcripts from a fasta file based on a list of accessions.

best,

~b

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Farbod Emami]

Hi Cheryl,

You can have a look at this, too.

https://www.biostars.org/p/209872/#211950