MEGAN - FASTA syntax for reading reads weights/magnitude

Question

[witold]

Dear All,

has anyone of you successfully loaded a Fasta file with read weights/magnitudes into Megan 5? Although I used both command line mode and sam2rma tool, there is no difference between annotation of weighted and not weighted Fastas. According to the manual, each of these Fasta header syntaxes should be accepted by the programme but there is no difference after running the programme (setting weights to 0 or 10E6 didn't work):

>CONTIG_id magnitude=13
>CONTIG_id weight=13
>CONTIG_id magnitude|13
>CONTIG_id weight|13

Lack of space or other sign than white space between CONTIG_id and magnitude in the header results in an error-the CONTIG cannot be found in the SAM file anymore.

Thank you in advance for any suggestions.

Answer 1

[daniel.huson]

All four variants should work, did you set Edit->Preferences->Use Magnitudes?

MEGAN requires that the first word in the header of a sequence and in the blast (or similar) matches is the same, so only extend the name of a read (or contig) before running blast (or whatever).

If you supply sequences to MEGAN (second field in Files tab of Blast Import dialog) then MEGAN will search for magnitudes there, otherwise MEGAN will look for a magnitude statement in the blast (or similar) matches.

If you setting the Edit->Preferences->Use Magnitudes item does not fix the problem, then please say in which format (e.g. XML, BlastX text) you are attempting to import stuff.

[witold]

Dear Daniel,

Thank you for your explanation.

Well, from the manual I understood the magnitudes can be read also if only present in a FASTA file, so thanks for sorting that out. Now if I import a BLAST tabular data from DIAMOND with added |weight=x in the first column it works perfectly fine but neither does sam2rma script nor manual SAM import work on the same data (this time converted to .sam with DIAMOND). The reads are simply read without concern of the magnitudes. Don't know what the exact issue is but it seems there is not full SAM interoperability yet.

Best,
W.