2.5 years ago by
Thanks guys for your answers - very much appreciated.
st.ph.n - to answer your question as to where I got the extract_splice_sites.py, I would say the script comes with the HISAT package. I think it basically helps to improve your mapping. One has to perfom this step although in my opinion performing this step is not a prerequisite, but I might be wrong. I wish I could go further to explain how it works, but I do not want to say this that I am not sure about - I am still new in this field of bioinformatics. I am just using bioinformatics tools to understand molecular biology at another level or from a different perspective. Thanks st.ph.n again for answering my other question about how to view the ouput file of hisat. Viewing the ouputfile is not just the only problem I have. I still struggle with production of the output file itself after running the script. In other words I still need to be able to instruct the script to produce the output file from which I can then be able to use IGV or samtools to view the mapped reads. So I really don't know how to deal with this (first) problem. Why is my script not producing the output file (please see my very first post).
To Renesh, thanks so much for answering the question that I never hoped I could overcome one day. So I will look at my gene annotation file (.gff3) to see if things are in order. If not, I will then have to change the "ID" to "id" and so on, and hopefully the script will run. If however the script will not run, I then drop the use of my .gff3 file downloaded from phytozome in favour of the .gtf file from EnsemblPlants database. So I have plenty of options and it's all thanks to you.
Just one more thing; what do I have to do in order to receive posts directly from my registerd e-mail so that I can make follow-ups almost immediately. I was lucky to come across your reply by just clicking on "messages". Thanks once again.
2.5 years ago by
LP • 20