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author yating-l
date Wed, 12 Apr 2017 17:43:55 -0400
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1 gbToFasta
2 ==========================================================
3 Galaxy wrapper for UCSC tools gbToFasta and raToTab. Convert GenBank records to fasta and create table with coding regions information for each mRNA record.
4
5 gbToFasta
6 ---------
7
8 gbToFaRa - Convert GenBank flat format file to an fa file containing
9 the sequence data, an ra file containing other relevant info and
10 a ta file containing summary statistics.
11
12 usage:
13 gbToFaRa filterFile faFile raFile taFile genBankFile(s)
14 where filterFile is definition of which records and fields
15 use /dev/null if you want no filtering.
16
17 $ gbToFaRa /dev/null gbfile.fa gbfile.ra gbfile.ta gbfile
18
19 raToTab
20 --------
21 raToTab - Create table with coding regions information for each mRNA record
22
23 usage:
24 raToTab -cols=acc,cds gbfile.ra gbfile.cds
25
26 Source code:
27 ============
28
29 http://hgdownload.cse.ucsc.edu/admin/exe/
30
31 Licence
32 -------
33 Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com).