Extract sequences in chromosome

Extract sequence in chromosome read tables with chromosome names and nucleotide positions. The sequences corresponding to the positions and offset are extracted from the fasta files with the chromosome sequences.

Manual :

1- if not already installed, install Perl free programming language

3- install Gnu parallel. (linux only)

4- unzip the software

5- copy your tables text (or csv) files in the “position” directory.

very important for parallel processing : the name of the table must be the chromosome number

example : chr_number.csv (19.csv, X.csv) with TAB separator

6- copy the fasta chromosome sequences in the "data" directrory.

very important : the fasta name must be the chromosome number

example : chr_number.fasta (19.fasta, X.fasta)

5- execute the software by the command : perl extract_sequence_xxx.pl tablePath length offset

for parallel processing : perl parallel_extract.pl (the number of cpu cores is set in the parallel_command_conf.txt file.

6- results are in the results directory.