I am attempting to design software for pulling out pathogen reads from either RNA-seq or WGS sequencing of human samples. The pipeline is centred around the NCBI taxonomy database and NCBI pathogen reference genomes, and now I am incorporating a component that will use FeatureCounts to process sciatica individual bam files mapped to pathogen genomes in order to determine expression levels of, say HPV transcripts, in cervical cancer etc when RNA-seq reads are the initial input. As such, I need a GTF or SAF format as described here: http://bioinf.wehi.edu.au/featureCounts/ Now, I can write a perl script to convert sciatica the GFF files available for viruses into a suitable GTF or SAF format, but I wanted to ascertain if viral and bacterial NCBI GTF or SAF files were already available somewhere, before I took the time and computational resources to convert 7,000 GFF files. Additionally, if anyone sciatica has already encountered this dilemma for any other reason and has a useful script that would be most helpful. Many thanks.
@seversond12: Have a look at this page: http://www.ensembl.org/info/website/upload/gff.html The type of fields(columns) available in both formats is the same, I therefore don't understand what you want to convert?
No comments:
Post a Comment