Hi all
I have blast results in tabular format comprising near about 0.5 Million entries having titles "qseqid; sseqid; qlen; slen; qstart; qend; sstart; send; evalue; length; pident; qcovs; bitscore; staxid; sscinames; scomnames; sskingdoms; stitle"
I want to analyse this data based on family, order, class, genus and species level in excel. How to import all taxonomic tree data for each taxon ids
Is there any perl, python script or tool available to do this analysis or fetch data from ncbi taxdb or other db?
suppose my data having more than 1 Million read which tool should i use for simple calculations like abundance and all (Excel only supports 1048576 raw in single sheet)
Hi ,
You can download MEGAN tool. it can directly take your blast results and plot various figures.
Cheers
Shab
http://ab.inf.uni-tuebingen.de/data/software/megan6/download/welcome.html
Thank you verymuch Shab
I tried MEGAN but i am looking for tool other than MEGAN
This is a troublesome job. I can see your results which do not contain gi number, if you want to obtain Taxonomy information, then need to use GI number (when you run blast+ program,you should use -show_gis options ) and Taxonomy database number one by one correspondence. Can be found here: ftp: //ftp.ncbi.nlm.nih.gov/pub/taxonomy/ and https://www.biostars.org/p/49738/, or you can google “ gi number to taxonomy ”.
Good luck.
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