Blast+ Output help

[Shorash]

Hey guys, I am trying new ways to speed up the Blasting process and have tried splitting my assembled transcriptome into small files and running a local blast with each one. I ran a sample file and it worked a lot faster than any other way I've tried, but I'm having a problem when attempting to load the output file into Blast2Go. Can anyone shed some light on the issue? I was hoping to run all the files, merge them all and load them up into Blast2Go fully blasted and ready to annotate. Thanks in advance for any help.

[Shorash]

Surely people have used Blast+?

[atcghelix]

Did you set the blast output to XML (-outfmt 5)?

Can you be more specific than "I'm having a problem when attempting to load the output file into Blast2Go."?

[Shorash]

Did you set the blast output to XML (-outfmt 5)?

Can you be more specific than "I'm having a problem when attempting to load the output file into Blast2Go."?

No, i didn't enter that command. I have an output file named x after performing Blastx on a file containing contigs. I'm attempting to load the file into Blast2Go software but receive an error saying the file needs to be in gzip format. Will the -outfmt 5 setting allow me to do so?

[atcghelix]

Are you running Blast2GO locally? Or on a web server somewhere?

I was under the impression that you needed to feed Blast2GO a blast file that was output in XML format, but I may be wrong.

[sphil]

Are you running Blast2GO locally? Or on a web server somewhere?

I was under the impression that you needed to feed Blast2GO a blast file that was output in XML format, but I may be wrong.

nope, I think the only output it can handly is XML since it is the most stable one.

[cliffbeall]

No, i didn't enter that command. I have an output file named x after performing Blastx on a file containing contigs. I'm attempting to load the file into Blast2Go software but receive an error saying the file needs to be in gzip format. Will the -outfmt 5 setting allow me to do so?

Gzip is a compression format that is separate from BLAST. You can convert your results file to gzip on the Linux or Mac command line, I'm sure there are also Windows tools.

[cascoamarillo]

Hey,
This is what it work for me so far. Using blast+ or blastall with xml as output. When the number of query seqs is quite high, load them into blas2go takes too much time, so I use blas2gopipe. I'm still working on this workflow, where I have some issues connecting to the database (why blast2go have so many problems with that?). Anyway, if you are able to run it, it will generate a projectfile (.dat) which you can open with blas2go desktop and run the annotation.