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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.
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Surely people have used Blast+? -
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."?Comment
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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?Originally posted by atcghelix View PostComment
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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.Comment
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nope, I think the only output it can handly is XML since it is the most stable one.Originally posted by atcghelix View PostComment
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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.Originally posted by Shorash View PostComment
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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.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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