Hello,
I have a list of sites (~9,000) that I need to pull out of the mouse genome in a .csv file as below;
Name, chromosome, start coordinate, end coordinate, length
Does any one know of an easy way to pull out these sequences that does not require me pulling them out one by one?
Thanks for any help you can provide,
Max
following .rar file contain Perl code that might be useful to you
in command prompt or terminal= perl convert.pl
it will output a file sequence_out.txt as result
check input file name also, you might also require to install Perl on windows system if it is not there you can get it from here https://www.perl.org/
Hi Max,
if you are looking for an user-friendly way to pulldown your sequences you can use either the ENSEMBL or the UCSC databases. With the UCSC table browser (https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=699297081_yHnueUSFkgzJnbaVkMqiv9hrU4uW) you can select the mouse genome, then select the Assembly track and finally paste the coordinates in the "define regions" window. You only need to change a bit the format of your table because you need this format:
Chromosome Start End
On the other hand if you were looking for a command line solution, I suggest to install the Bedtools suite (https://bedtools.readthedocs.io/en/latest/) and use the getfasta command. You need to format your table as I mentioned before and then you need to download the FASTA file of the genome. Then the command is quite straightforward and it is well explained in the manual.
I hope this helps!
Have a nice day
Riccardo
Bioinformatician @ www.sequentiabiotech.com
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