Skip to content
Snippets Groups Projects
Commit f9360ffe authored by Ahmed Hassan Hussein Hefny Mahmoud's avatar Ahmed Hassan Hussein Hefny Mahmoud
Browse files

Updated README

parent cd120023
No related branches found
No related tags found
1 merge request!22Updated README
# Extract transcript sequences
Project aim:
### Project aim:
Given a gtf specification of transcript exon/intron structures and the genome sequence, construct the nucleotide sequence of the transcripts and add poly(A) tails.
Input:
__Input:__
* Gtf file with exon/intron structures of transcripts
* File with genome sequence
* Length of the poly(A) tail
* Dictionary of expected nucleotide frequencies in poly(A) tail
* Output: fasta-formatted file of transcript sequences
Output:
For each transcript, the list of exons should be traversed from 5' to 3', the sequences of the exons need to be extracted from the genome given the coordinates and then pasted together. At the end, a tail of the specified length should be added at the 3' end of the transcript, given a vector of mono-nucleotide frequencies (of course, the frequency of A's will be much higher than of any other nucleotide).
__Output:__
For each transcript, the list of exons should be traversed from 5' to 3', the sequences of the exons need to be extracted from the genome given the coordinates and then pasted together. At the end, a tail of the specified length should be added at the 3' end of the transcript, given a vector of mono-nucleotide frequencies (of course, the frequency of A's will be much higher than of any other nucleotide).
## Design plan
......@@ -52,7 +48,7 @@ e. Output the final transcript sequences as a .fasta file. (Final Output)
## License
[MIT](https://choosealicense.com/licenses/mit/) license, Copyright (c) 2021 Zavolan Lab, Biozentrum, University of Basel
[MIT](https://choosealicense.com/licenses/mit/) license, Copyright (c) 2022 Zavolan Lab, Biozentrum, University of Basel
## Contributers
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment