Question: Very few assigned reads in MEGAN
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gravatar for dazhudou1122
3.2 years ago by
dazhudou112250
dazhudou112250 wrote:

Hey guys,

I have some RNA-Seq reads that I want to blast and reconstruct metabolic pathways on. Since the RNA-seq results are actually DNA sequences, I used the DIAMOND Blast-Megan6-SEED annotation workflow to achieve my goal. But I am having some issues: with each samples having ~20000 aligned reads, I only got less than a hundred assigned in Megan. I have loaded the 2015 and 2016 GI mapping file (taxonomy) and SEED/KEGG files but I am still getting these errors. Any ideas guys?

Some samples lines in the m8 files: SRR317086.69 gi|958165026|gb|ALQ41808.1| 69.6 23 7 0 75 7 349 371 1.8e-02 33.5 SRR317086.69 gi|929734199|gb|ALF26823.1| 69.6 23 7 0 75 7 349 371 1.8e-02 33.5 SRR317086.69 gi|929726675|gb|ALF19302.1| 69.6 23 7 0 75 7 349 371 1.8e-02 33.5 SRR317086.69 gi|657895453|ref|WP_029598743.1| 69.6 23 7 0 75 7 349 371 1.8e-02 33.5 SRR317086.69 gi|552906288|ref|WP_023037794.1| 69.6 23 7 0 75 7 349 371 1.8e-02 33.5 SRR317086.69 gi|511278547|ref|WP_016339635.1| 69.6 23 7 0 75 7 349 371 1.8e-02 33.5 SRR317086.69 gi|499325845|ref|WP_011016337.1| 69.6 23 7 0 75 7 349 371 1.8e-02 33.5 SRR317086.69 gi|496071367|ref|WP_008795874.1| 69.6 23 7 0 75 7 349 371 1.8e-02 33.5 SRR317086.69 gi|492644446|ref|WP_005909615.1| 69.6 23 7 0 75 7 349 371 1.8e-02 33.5 SRR317086.69 gi|492587891|ref|WP_005896039.1| 69.6 23 7 0 75 7 349 371 1.8e-02 33.5 SRR317086.69 gi|492573108|ref|WP_005890553.1| 69.6 23 7 0 75 7 349 371 1.8e-02 33.5 SRR317086.69 gi|19703702|ref|NP_603264.1| 69.6 23 7 0 75 7 349 371 1.8e-02 33.5 SRR317086.69 gi|958165026|gb|ALQ41808.1| 83.3 24 4 0 3 74 289 312 5.7e-06 45.1 SRR317086.69 gi|929734199|gb|ALF26823.1| 83.3 24 4 0 3 74 289 312 5.7e-06 45.1 SRR317086.69 gi|929726675|gb|ALF19302.1| 83.3 24 4 0 3 74 289 312 5.7e-06 45.1 SRR317086.69 gi|657895453|ref|WP_029598743.1| 83.3 24 4 0 3 74 289 312 5.7e-06 45.1 SRR317086.69 gi|552906288|ref|WP_023037794.1| 83.3 24 4 0 3 74 289 312 5.7e-06 45.1 SRR317086.69 gi|511278547|ref|WP_016339635.1| 83.3 24 4 0 3 74 289 312 5.7e-06 45.1 SRR317086.69 gi|499325845|ref|WP_011016337.1| 83.3 24 4 0 3 74 289 312 5.7e-06 45.1 SRR317086.69 gi|496071367|ref|WP_008795874.1| 83.3 24 4 0 3 74 289 312 5.7e-06 45.1 SRR317086.69 gi|492644446|ref|WP_005909615.1| 83.3 24 4 0 3 74 289 312 5.7e-06 45.1 SRR317086.69 gi|492587891|ref|WP_005896039.1| 83.3 24 4 0 3 74 289 312 5.7e-06 45.1 SRR317086.69 gi|492573108|ref|WP_005890553.1| 83.3 24 4 0 3 74 289 312 5.7e-06 45.1 SRR317086.69 gi|19703702|ref|NP_603264.1| 83.3 24 4 0 3 74 289 312 5.7e-06 45.1 SRR317086.500 gi|983310289|ref|WP_060495679.1| 45.0 20 11 0 11 70 289 308 6.3e+00 25.0 SRR317086.500 gi|644872521|ref|WP_025374958.1| 45.0 20 11 0 11 70 289 308 6.3e+00 25.0 SRR317086.500 gi|511541261|ref|WP_016361212.1| 45.0 20 11 0 11 70 289 308 6.3e+00 25.0 SRR317086.521 gi|983310289|ref|WP_060495679.1| 45.0 20 11 0 66 7 289 308 6.3e+00 25.0 SRR317086.521 gi|644872521|ref|WP_025374958.1| 45.0 20 11 0 66 7 289 308 6.3e+00 25.0 SRR317086.521 gi|511541261|ref|WP_016361212.1| 45.0 20 11 0 66 7 289 308 6.3e+00 25.0 SRR317086.527 gi|983524772|ref|WP_060676525.1| 45.8 24 13 0 3 74 875 898 6.1e+00 25.0 SRR317086.527 gi|983310337|ref|WP_060495727.1| 45.8 24 13 0 3 74 875 898 6.1e+00 25.0 SRR317086.527 gi|958165889|gb|ALQ42671.1| 45.8 24 13 0 3 74 875 898 6.1e+00 25.0 SRR317086.527 gi|929732382|gb|ALF25006.1| 45.8 24 13 0 3 74 875 898 6.1e+00 25.0 SRR317086.527 gi|19703859|ref|NP_603421.1| 45.8 24 13 0 3 74 875 898 6.1e+00 25.0

rna-seq • 832 views
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