rearrange columns with Galaxy

Question: rearrange columns with Galaxy

2.6 years ago by

Mic • 70

Australia

Mic • 70 wrote:

Hello, I have the following GFF file:

    ##gff-version 3
    #!gff-spec-version 1.21
    #!processor NCBI annotwriter
    #!genome-build Assembly 2.2 of Bactrocera tryoni genome
    #!genome-build-accession NCBI_Assembly:GCA_000695345.1
    ##sequence-region JHQJ01000001.1 1 3181581
    ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=59916
    JHQJ01000001.1  Genbank region  1   3181581 .   +   .   ID=id0;Dbxref=taxon:59916;country=Australia: Gosford%2C NSW;gbkey=Src;lat-lon=33.86 S 151.21 E;mol_type=genomic DNA;note=inbred lab stock%3B collected in 1990s;sex=male;strain=bent wings;tissue-type=whole body
    ##sequence-region JHQJ01000002.1 1 1701813
    ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=59916
    JHQJ01000002.1  Genbank region  1   1701813 .   +   .   ID=id1;Dbxref=taxon:59916;country=Australia: Gosford%2C NSW;gbkey=Src;lat-lon=33.86 S 151.21 E;mol_type=genomic DNA;note=inbred lab stock%3B collected in 1990s;sex=male;strain=bent wings;tissue-type=whole body
    ##sequence-region JHQJ01000003.1 1 1550466

I would like to use RnaChipIntegrator, but it requires as input the following columns:

    Column  Name        Description
    1       ID          Name used to identify the gene in the output
    2       chr         Chromosome name
    3       start       Start position of the gene
    4       end         End position of the gene
    5       strand      Must be either '+' or '-'
    6       diff_expr   Optional: indicates gene is differentially expressed (1) or not (0)

How can convert the GFF file to the supported input file for RnaChipIntegrator?

Thank you in advance.

Mic

galaxy • 786 views

ADD COMMENT • link •

modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by Mic • 70

2.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Tools in the group Text Manipulation can be used:

Remove the header lines with Select ("Not Matching" with expression "^#" - no quotes)
Extract just the columns needed with Cut

Thanks, Jen, Galaxy team

ADD COMMENT • link modified 2.6 years ago • written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you, but how do I rearrange the columns i.e. the 1st column in GFF is the 2nd column in RnaChipIntegrator?

ADD REPLY • link written 2.6 years ago by Mic • 70

Hi :) Maybe you could try extracting each column (or group of columns) separately with the cut tool as suggested above and then use the paste tool (also in Text manipulation section) to paste them back together side by side in the order you want?

ADD REPLY • link written 2.6 years ago by Saskia Hiltemann • 70

Similar posts • Search »