Hi MEGAN community,
I want to analysis the contigs which didn’t result in any hits using BLAST, but there isn’t any information about the sequences in this leaf!
I’m able to extract the sequences for all others leaves, but for “no Hits” there is no information, not even their IDs.
Thank you in advance!
What kind of file? Meganized DAA or RMA?
Thank you Daniel for reply, I’m working with RMA files.
I just tested this on one of my RMA files. I can definitely extract reads assigned to the no hits node. Did you supply the FastA file when importing the alignments? What does the inspector window show you?
You should be able to see the reads in it, like this:
Thank you dear Daniel,
Yes I supplied the FastA files:
I can’t see the “no hit node”, but I’m able to extract the reads for all other nodes.
and as it’s shown in this screenshot, the number of reads in the FastA file is 10659:
Thanks again
Which aligner did you use to align the contigs? It looks like either the aligner or MEGAN did not include the unaligned reads in the file.
I used BLAST for alignment, blastX results don’t include the unaligned contigs, but when I supply the FastA file the no hit reads don’t count by MEGAN?
Thank you,
Sorry - Megan bases it’s analysis on the alignment file - I will look into implementing an additional calculation that determines which reads are not mentioned in the alignment file and adds them to the rma file
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Thank you so much 