Closed worsteggs closed 3 years ago
@nabeel-bioinfo Thanks for replying! I have seen the web interface, and it's a nice work!
But now I have another question. Since I use human data, how can I get the CDS_info.tab file like the yeast? Can I convert to it directly from the human genome gff3 file download from gencode project?
Thanks again for your nice work!
I get the CDS_info.tab file successfully by converting directly from the human genome gff3 file. I'll close this issue. Thanks for your help!
You can run the first script and add the following arguments. -s indicates that A-site profiles be generated -p is the file containing the offset table for yeast as shown in the paper. This file is present in the data_files directory.
python src/asite_ip_preprocess.py -m 20 -x 35 -g data_files/sacCer3/CDS_info.tab -e data_files/sacCer3/sacCer3_R64-2-1_genome.fa -i input.sam -s Yes -p data_files/sacCer3/A-site_IP_offset_table_yeast.tab
There is now a web interface based on these scripts to generate A-site profiles. Please visit https://a-site.vmhost.psu.edu/.