using a new attribute in a gff file

Dolev Rahat · 03-27-2014, 12:23 PM

Hello

I am trying to use HTSeq to map counts from an RNASeq assay in order to preform a diffrential expression analysis on lincRNAs.
I have a lisf of the lincRNAs I want to use in the analysis in a BED file, which I converted into a gff file using Galaxy's bed_to_gtf_convertor script.
An example attribute line from my file:
exon linc|3P|XLOC_000004|TCONS_00000005:2.63081|141AA|61AA|;
The problem is that lincRNAs are not a standard attribute in gff/gtf files attribute columns, so when I attempted run the HTSeq.counts setting idattr to 'linc', but recived the following error message:

“Feature linc|3P|XLOC_000004|TCONS_00000005:2.63081|141AA|61AA| does not contain a 'linc' attribute”

since the string 'linc' does appear in many rows of my file's attribute column, I suspect something may be wrong with the attribute strings formatting (wrong delimters etc.), but am not sure what would be the correct format.

I will appreciate any advice on how to format these strings, or any other ideas on how I can make the attribute column useable

Thanks in advance

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03-27-2014, 12:23 PM	#1
Dolev Rahat Junior Member Location: Jerusalem Israel Join Date: Mar 2014 Posts: 2	using a new attribute in a gff file Hello I am trying to use HTSeq to map counts from an RNASeq assay in order to preform a diffrential expression analysis on lincRNAs. I have a lisf of the lincRNAs I want to use in the analysis in a BED file, which I converted into a gff file using Galaxy's bed_to_gtf_convertor script. An example attribute line from my file: exon linc\|3P\|XLOC_000004\|TCONS_00000005:2.63081\|141AA\|61AA\|; The problem is that lincRNAs are not a standard attribute in gff/gtf files attribute columns, so when I attempted run the HTSeq.counts setting idattr to 'linc', but recived the following error message: “Feature linc\|3P\|XLOC_000004\|TCONS_00000005:2.63081\|141AA\|61AA\| does not contain a 'linc' attribute” since the string 'linc' does appear in many rows of my file's attribute column, I suspect something may be wrong with the attribute strings formatting (wrong delimters etc.), but am not sure what would be the correct format. I will appreciate any advice on how to format these strings, or any other ideas on how I can make the attribute column useable Thanks in advance