Question: How to create EGFP GTF file?
0
gravatar for Payal
18 months ago by
Payal40
Payal40 wrote:

Hi,

I am analyzing RNA Seq data with EGFP. I need to get the count of EGFPs for samples. So I am thinking to align the fastq files to the EGFP sequence concatenated to the reference genome and then get the counts using HTseq counts. I have the EGFP.fa file, but how to create the EGFP GTF file as thats required for Htseq counts and for annotation!!

EGFP Sequence:(Is this ok?)

>EGFP
ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAA
GTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGC
TGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAG
CAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTA
CAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGG
ACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAAC
GGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACAC
CCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACG
AGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAA

GTF: (Is this ok?)

EGFP    EGFP    exon    1   720 0.000000    +   .   gene_id "EGFP"; transcript_id "EGFP";

Thanks, Payal

rna-seq • 1.1k views
ADD COMMENTlink modified 18 months ago by genomax74k • written 18 months ago by Payal40
1

If your EGFP.fa file looks like this

>EGFP
AGCTCAGATCGATAGCTACG

then make your GTF file to have a line at the end with something like this (chromosome name EGFP needs to match in both, add right length of sequence in place of 1000)

EGFP    unknown exon    1   1000   .       +       .       gene_id "EGFP"; gene_name "EGFP"
ADD REPLYlink modified 18 months ago • written 18 months ago by genomax74k

This helped me a lot.

Just another update on this: You'll need to add "transcript_id" to the GTF file to get it to work.

ADD REPLYlink written 11 months ago by deeptimanchatterjee0
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