On 10/10/2011 04:45 PM, Ian Donaldson wrote:
Thanks, but not quite what i need.
If i start with two intervals:
chr1 500 1000 geneA . +
chr1 2000 2500 geneB . -
I want to add via, e.g. 'Compute', the TSS position to the end of each line.
The desired result being:
chr1 500 1000 geneA . + 500
chr1 2000 2500 geneB . - 2500
This is because geneA is on the '+' strand and geneB is on the '-' strand.
Hi Ian
Have you tried
"Filter and Sort"-> "Filter" data on any column using simple expressions
and create two lists containing all genes on the '+' strand and alles
genes on the '-' strand.
followed by
"Text Manipulation"-> "Cut" columns from a table
using 'c1,c2,c3,c4,c5,c6,c2' for the list with all genes on the '+'
strand
and
using 'c1,c2,c3,c4,c5,c6,c3' for the list with all genes on the '-'
strand
and then you can create a single list again with
"Text Manipulation"-> "Concatenate" datasets tail-to-head
I guess this is waht you want, isn't-it?
Regards, Hans
Thanks,
Ian
________________________________
From: Daniel Blankenberg [[email protected]]
Sent: 10 October 2011 14:34
To: Ian Donaldson
Cc: [email protected]
Subject: Re: [galaxy-user] Q about 'Compute' tool
Hi Ian,
Under Operate on Genomic Intervals, you can try the "Get Flanks" tool; you can
request upstream, downstream, or both of your provided regions. Please let us know if you
need additional assistance.
Thanks for using Galaxy,
Dan
On Oct 10, 2011, at 6:35 AM, Ian Donaldson wrote:
Hi,
Can 'if' statements by used in 'Text manipulation'> 'Compute'?
The reason is that i have a interval file of UCSC genes, i want to identify the
TSS of each and make a new interval reflecting the TSS position for each gene.
But because the TSS of a '-' stranded gene is actually the 'end' coord i want
to be able to check the strand in the compute statement.
Is this possible or is there an easier way to do this inside GALAXY?
Thank you,
Ian
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