Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Reads file(s) not given or found, RMA file will not contain read sequences

    So I completed a BLAST run where I've matched my query 16S rRNA sequences with a custom 16S rRNA database with the following command on Unix:

    /usr/local/blast/2.2.29/bin/blastn -query data/output_data/13L29Trimmed.fasta -db data/database/16sdatabaseBLAST -out output_data/13L29Blasted.blastn -evalue 1e-10 -num_threads 6 -outfmt 7 &

    After completing the BLAST, I received a 1.1 GB blastn file as expected. A bioinformatics friend then told me to use MEGAN to process my BLAST results, which I did. The first thing I tried to do was to import my BLAST file into MEGAN. Even after providing MEGAN with the gi mapping file it needs to process the BLAST result, I get the following error:

    Reads file(s) not given or found, RMA file will not contain read sequences

    Afterwards, I find that although my reads have been successfully matched, that none of them were actually assigned.

    After doing some troubleshooting, I think it's related to the output format I tried to set for my BLAST run. Reading through the manual, I found that the output option 7, the one I used, should be suitable for MEGAN processing. However, I can't get MEGAN to assign the reads.

    If someone can help me see what I'm doing wrong, I'd much appreciate it!

Latest Articles

Collapse

  • 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
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X