Question: list to one fasta file
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gravatar for c.chakraborty
13 days ago by
c.chakraborty110
c.chakraborty110 wrote:

Dear all, I used biomaRt to retrieve the 3'UTR sequences of 1527 transcpts, using their refseq ids:

for (i in uniquetrans[,1]{
            sequences[i] = getSequence(id =i, type= "refseq_mrna", seqtype= "3utr", mart=ensembl, verbose= FALSE
 }

The sequences were retreived and all, but now, I have a problem in converting the list into a file. I tried exportFASTA(), but it works for a single sequence at time which is irritating. I also tried lapplys such as

 lapply(sequences, write, "test.txt", append=TRUE, ncolumns=1527)

and I got the sequences, but they don't have a header. What do i do now. I can write a for loop and convert each one in a separate text file, but it is so cumbersome! Please help. Regards, Chaitali

biomar R fasta • 69 views
ADD COMMENTlink written 13 days ago by c.chakraborty110
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