Hello everyone!
I am a new user to DIAMOND and MEGAN6. This question may sounds silly but I have tried so hard these days to try to import a DIAMOND alignment result file into MEGAN and visualize it.
So, I have generate different format type including .daa file, .sam file, .m0 file , .xml file and .m8 file.
I have tried to import them into MEGAN6 through the File>Import From BLAST and FILE>Meganize DAA File for the .daa files. How ever, only two nodes appear and all the reads are in the node “Not assigned”.
I have searched online for solution, from Biostar, Stackoverflow and here in the MEGAN community. However, I still cannot solve it…
I am aligning my fastq file to the NCBI nr database with the following code:
diamond blastx --query ./BP7-A/Sample.fastq --db nr --daa ./DAA/S1000_1.daa
I have followed the instruction in here Generic pipeline using DIAMOND and MEGAN6 but I still got only two nodes.
I have already download the GI-to-NCBI mapping file and also the accession mapping file.
The following are some of the reads inside the m8, sam and xml file.
.m8 file:
HWI-C00135:230:CAG5BANXX:7:2309:15572:61333 CDA22218.1 84.8 33 5 0 3 101 440 472 1.8e-07 62.8
HWI-C00135:230:CAG5BANXX:7:2309:15572:61333 WP_068962080.1 80.6 31 6 0 3 95 444 474 9.7e-06 57.0
HWI-C00135:230:CAG5BANXX:7:2309:15572:61333 WP_046147429.1 63.6 33 12 0 3 101 440 472 2.4e-04 52.4
HWI-C00135:230:CAG5BANXX:7:2309:15572:61333 WP_068185816.1 63.6 33 12 0 3 101 440 472 3.1e-04 52.0
.sam file:
@HD VN:1.5 SO:query
@PG PN:DIAMOND
@mm BlastX
@CO BlastX-like alignments
@CO Reporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length, ZF: frame, ZS: query start DNA coordinate
HWI-C00135:230:CAG5BANXX:7:2309:15572:61333 0 CDA22218.1 440 255 33M * 0 0 EQIHALTRIDRWFLNKLHNIVQTADELESYNQL * AS:i:62 NM:i:5 ZL:i:1072 ZR:i:151 ZE:f:1.8e-07 ZI:i:84 ZF:i:3 ZS:i:3 MD:Z:D3D9E6R6K4
HWI-C00135:230:CAG5BANXX:7:2309:15572:61333 0 WP_068962080.1 444 255 31M * 0 0 EQIHALTRIDRWFLNKLHNIVQTADELESYN * AS:i:56 NM:i:6 ZL:i:1079 ZR:i:136 ZE:f:9.7e-06 ZI:i:80 ZF:i:3 ZS:i:3 MD:Z:D3E2K6Y6A6G2
HWI-C00135:230:CAG5BANXX:7:2309:15572:61333 0 WP_046147429.1 440 255 33M * 0 0 EQIHALTRIDRWFLNKLHNIVQTADELESYNQL * AS:i:52 NM:i:12 ZL:i:1074 ZR:i:124 ZE:f:2.4e-04 ZI:i:63 ZF:i:3 ZS:i:3 MD:Z:D6K2K3Q2Y2I3GA3FSKI
. xml file:
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_query-ID>Query_1</Iteration_query-ID>
<Iteration_query-def>HWI-C00135:230:CAG5BANXX:7:2309:15572:61333</Iteration_query-def>
<Iteration_query-len>101</Iteration_query-len>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gnl|BL_ORD_ID|460</Hit_id>
<Hit_def>CDA22218.1</Hit_def>
<Hit_accession>460</Hit_accession>
<Hit_len>1072</Hit_len>
<Hit_hsps>
I am sorry for such a long passage, but I really need some help on it. Thank you very much!
