Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Blast+ Output help

    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.

  • #2
    Surely people have used Blast+?

    Comment


    • #3
      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


      • #4
        Originally posted by atcghelix View Post
        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?

        Comment


        • #5
          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


          • #6
            Originally posted by atcghelix View Post
            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.

            Comment


            • #7
              Originally posted by Shorash View Post
              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.

              Comment


              • #8
                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

                Latest Articles

                Collapse

                • seqadmin
                  Current Approaches to Protein Sequencing
                  by seqadmin


                  Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
                  04-04-2024, 04:25 PM
                • seqadmin
                  Strategies for Sequencing Challenging Samples
                  by seqadmin


                  Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                  03-22-2024, 06:39 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, 04-11-2024, 12:08 PM
                0 responses
                30 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 04-10-2024, 10:19 PM
                0 responses
                32 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 04-10-2024, 09:21 AM
                0 responses
                28 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 04-04-2024, 09:00 AM
                0 responses
                52 views
                0 likes
                Last Post seqadmin  
                Working...
                X