Question: Are there any tools that can create a very basic GTF file from contig sequences (no annotations really needed) ?
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gravatar for O.rka
5 weeks ago by
O.rka90
O.rka90 wrote:

I want to use featureCounts but it requires a GTF file. I really like the following two parameters for minimum percent identity and minimum spatial coverage (I think that's what these are below?)

--fracOverlap <float> Minimum fraction of overlapping bases in a read that is required for read assignment. Value should be within range [0,1]. 0 by default. Number of overlapping bases is counted from both reads if paired end. Both this option and '--minOverlap' option need to be satisfied for read assignment.

--fracOverlapFeature <float> Minimum fraction of overlapping bases in a feature that is required for read assignment. Value should be within range [0,1]. 0 by default.

I am going to work on a pipeline that feeds into this but sometimes I will just be mapping reads to contigs that don't have any features.

Is there a tool that takes in a fasta file (e.g. contigs) and converts them into a very basic GTF file just so the featureCounts pipeline can be used?

mapping assembly • 113 views
ADD COMMENTlink written 5 weeks ago by O.rka90
1

Typically, one uses a GTF file to represent annotation. Is your contig annotated? If not, you can create a 'fake' GTF file with just one feature that goes from the first nt to the last nt of the contig. You won't need the sequence for this but the name, length of the contig. The specs for GTF file are here: http://mblab.wustl.edu/GTF22.html

ADD REPLYlink written 29 days ago by vkkodali1.1k
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