taxonomic classification

Question

[weimabri]

Good day.

I did an RNAseq, which I assembled by Trinity, then I did a BlastN. BlastN results filtered and organized in a .xlsx file What software can I use to make a taxonomic classification from this file?

# query subject_id  subject_def pident  align_length    qstart  qend    sstart  send    bitscore    e_value
TRINITY_DN91_c0_g1_i4   gi|1218258742|ref|XM_021852686.1|   [Candida] intermedia strain CBS 141442 genome assembly, chromosome: I   117 142 1018    1157    247055  246916  121.15  4.79e-22
TRINITY_DN91_c0_g1_i4   gi|1218258740|ref|XM_021852685.1|   [Candida] intermedia strain CBS 141442 genome assembly, chromosome: I   117 142 1018    1157    247055  246916  121.15  4.79e-22
TRINITY_DN91_c0_g1_i4   gi|122937760|gb|EF173372.1| [Enterobacter] lignolyticus strain G5 chromosome, complete genome   420 434 90  523 110398  110831  725.01  0.00e+00
TRINITY_DN91_c0_g1_i4   gi|122937760|gb|EF173372.1| [Enterobacter] lignolyticus strain G5 chromosome, complete genome   420 434 90  523 208214  208647  725.01  0.00e+00

Answer 1

[Istvan Albert]

A tool like MEGAN can combine the various BLAST hits into hierarchical classification model

https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/

[weimabri]

The result of the BlastN, I have it in this format. BLASTN_NTAgo2021_Trinity_clean_Com06.Trinity.fasta.xml.tab

But the MEGAN6 does not identify it as a BLAST format, Do you know of a way to change it to a format that identifies Megan?

[Istvan Albert]

It needs to have certain columns, look up what those are. There are also various other input formats that you may be able to change your data into.