Hi there,
I'm new in bioinformatics tools and I need help. 
I tell you what I have done :)

I have an assembly from Trinity and I wanted to know the  CG content of each assembly so I generated a file with this information and I imported to R. 

Then, I calculated the CG content of all my contigs in R by doing:

    ## load data
    data= read.table("CG_content_contig.txt", header = T)

    ## Create a new variable called CG
    data$CG <- (data$C+data$G)/(data$A+data$C+data$G+data$T)

    ## Create a file with CG content > 23%
    CG_content_more_than_23 <- data[which(data$CG > '0.23'), ]

    ## Create a file only with the names of the contigs
    name_contigs <- CG_content_more_than_23$chr

    ## Download .txt file. 
    write.table(name_contigs, file="name_contigs.txt", row.names=FALSE, sep='\t')

As you see, I have created a file with those contigs with an CG content higher than 23%. I have uploaded this file (name_contigs.txt) to my server in order to work with it. It looks like this:

    TRINITY_DN134693_c0_g1_i1
    TRINITY_DN109669_c0_g1_i1
    TRINITY_DN109679_c0_g1_i1
    TRINITY_DN114999_c0_g1_i1
    TRINITY_DN114910_c0_g1_i1

I have a .fq file that looks like this:

    >TRINITY_DN134617_c0_g1_i1
     AATAAAAATAAATAAAAATCAATAAAAATATTATAATACAATATAATATAAAATAATATAAAAATTCTACAATAAGAATAAAGTATAATTTTTTAGATTATAAGAGGATATGTTAATACATAGTATTCTGTTTGTTATTGTAGAAAAAACATACAGAAACTTTTTGTATATATAGTCTCATTTTATATATATAAATAAAAATGAACATTAATGAAATGAAATTAAGAGTCGTTTTATTAAAAATAGCTATAAAAAATAACAACA

    >TRINITY_DN134643_c0_g1_i1
    GCATGGTAGTAAAGTATAATGACATAGCAAAAATATTTAAAATAAAAAAAAATTACTATTATAATTTTTTCTGTATAACATAAACGTTTTTAATGATATTATATTAATTACATATAAAAATAGCATAATAAAAATATTTAGTTATAAAATTTATTATTTTATTTTTTTTTTTTTGTTATATACTTTCTCAGAACATTAATTTGTCATCAGTTCTATTATATTGATAAACTATTCAATTGCTTTAATA


What I want to do is to keep only the contigs that are NOT in the .txt file. 

Maybe I should create a pipeline with grep command?


You should use `faSomeRecords` [utility from Jim Kent][1] (UCSC, linux binary linked). Add execute permissions after download `chmod u+x faSomeRecords`.

    faSomeRecords - Extract multiple fa records
    usage:
       faSomeRecords in.fa listFile out.fa
    options:
       -exclude - output sequences not in the list file.


  [1]: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faSomeRecords