Name: Diamond
Owner: Hurwitz Lab
Description: Utilizes Diamond to generate BlastX data from sequence reads
Created: 2016-10-19 19:36:57.0
Updated: 2016-10-19 19:49:41.0
Pushed: 2016-11-17 21:05:37.0
Homepage: null
Size: 7
Language: Shell
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This program utilizes Diamond to generate BlastX data from sequence reads. The default reference database used in this analyses is Swiss-Prot and will automatically be downloaded for use. The Diamond output files (.dout) are in BlastX format and Swiss-Prot ids are extracted from the results (.ids). The Swiss-Prot ids are assigned NCBI taxonomy ids (.taxid). Counts are then generated for both taxonomy (tax.count) and Swiss-Prot ids (id.count). See “Expected Results” section for examples of output files.
If you want to use a reference other than Swiss-Prot, a Diamond database must be generated.
$ diamond makedb --in nr.faa -d nr
This program is optimized for the default settings which uses Swiss- Prot reference database. If using the default settings, the above command is not necessary.
Before Start:
A file named 'list' needs to be created in the directory containing your Fasta/q files. The program will read 'list' in order to know what files need to be analyzed. Below is an example of how 'list' could be created:
$ cd $FASTA_DIR
$ ls
file1.fa file2.fa file3.fa
$ ls *.fa > list
$ cat list
file1.fa
file2.fa
file3.fa
Instructions:
1) Edit the VARIABLE DECLARATION section at the top of submit.sh to include the paths for the FASTA_DIR (location of fasta files and 'list') and DIAMOND_DIR (location of Diamond executable). Other variables can be edited as needed such as THREADS (# of CPUs). PRESETS only need to be changed if you are not using the default Swiss-Prot database.
2) Edit PBS ALLOCATIONS section at the top of diamondx.sh (found in script directory). Here is an example of a complete PBS ALLOCATIONS:
#---- PBS ALLOCATIONS ----
#PBS -W group_list=bhurwitz
#PBS -q standard
#PBS -l select=1:ncpus=4:mem=15gb
#PBS -l pvmem=12gb
#PBS -l place=pack:shared
#PBS -l walltime=24:00:00
#PBS -l cput=24:00:00
#PBS -M jamesthornton@email.arizona.edu
#PBS -m bea
Note that group_list, -q standard, and -M email, should be edited to include your group name, queue type, and email respectively.
3) Execute submit.sh
$ ./submit.sh
Expected Results:
Diamond Blast Output (.dout) -
[jamesthornton@service1 diamond_out]$ head IonXpress_017.dout
3932-6 sp|Q99959|PKP2_HUMAN 72.7 33 9 0 106 8 472 504 4.4e-07 53.9
3932-6 sp|Q05481|ZNF91_HUMAN 80.0 30 6 0 90 1 1159 1188 1.7e-06 52.0
3932-6 sp|Q7Z5D8|NANGN_HUMAN 76.7 30 7 0 105 16 332 2.2e-06 51.6
3932-6 sp|Q86V71|ZN429_HUMAN 74.1 27 7 0 97 17 648 674 9.2e-05 46.2
5017-5 sp|B2RM62|UVRC_PORG3 60.0 40 16 0 5 124 55 94 1.8e-06 52.0
5017-5 sp|Q7MTG8|UVRC_PORGI 60.0 40 16 0 5 124 54 93 1.8e-06 52.0
5017-5 sp|Q04EZ7|UVRC_OENOB 55.0 40 18 0 5 124 53 92 1.2e-05 49.3
5017-5 sp|B3E394|UVRC_GEOLS 58.3 36 15 0 17 124 55 90 4.5e-05 47.4
5017-5 sp|Q8REL0|UVRC_FUSNN 55.0 40 18 0 5 124 48 87 4.5e-05 47.4
5017-5 sp|Q14I60|UVRC_FRAT1 55.0 40 18 0 5 124 59 98 2.2e-04 45.1
Swiss-Prot ID list (.ids) -
[jamesthornton@service1 diamond_out]$ head IonXpress_017.ids
PKP2_HUMAN
ZNF91_HUMAN
NANGN_HUMAN
ZN429_HUMAN
UVRC_PORG3
UVRC_PORGI
UVRC_OENOB
UVRC_GEOLS
UVRC_FUSNN
UVRC_FRAT1
Taxid Assignment (.taxid) -
[jamesthornton@service1 diamond_out]$ head IonXpress_017.taxid
PKP2_HUMAN = 9606
ZNF91_HUMAN = 9606
NANGN_HUMAN = 9606
ZN429_HUMAN = 9606
UVRC_PORG3 = 431947
UVRC_PORGI = 242619
UVRC_OENOB = 203123
UVRC_GEOLS = 398767
UVRC_FUSNN = 190304
UVRC_FRAT1 = 393115
Taxid Counts (tax.count) -
[jamesthornton@service1 diamond_out]$ head IonXpress_017_tax.count
9565 16
378806 4
135720 9
9595 91
138119 20
1245 2
9833 37
323850 33
9546 1
224324 106
Swiss-Prot ID Counts (id.count) -
[jamesthornton@service1 diamond_out]$ head IonXpress_017_id.count
TRMFO_RHIL3 2
GCDH_MACFA 2
RL16_MYCPA 1
LOLD_XANOR 1
XYLG_RALSO 1
FABZ_VEREI 1
PANB_NITOC 1
UVRC_FRATM 2
SECA_GEOMG 3
Y1095_PORGI 1
For more information on Diamond see the user manual at http://ab.inf.uni-tuebingen.de/data/software/diamond/download/public/manual.pdf
Diamond publication can be found here: http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3176.html