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nabeel-bioinfo / Asite_IP_method

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How to generate the A-site read density profiles? #1

Closed worsteggs closed 3 years ago

nabeel-bioinfo commented 3 years ago

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/.

worsteggs commented 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!

worsteggs commented 3 years ago

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!