Export the table from the Long read inspector

Feature Requests
#1

Dear MEGAN members:

I am new to this program, and I am running it to see the blastn results of my assembled contigs. Then, I found that with the Long read inspector, the table (including read, length, assignment, %cover, and #alignments) is the one I would like to export as a table. However, I tried to find how to export that, and it was in vain. I think I might missed something. Thus, could anyone help me to export this table?

Thank you for your kind help!

Best wishes,

CY

#2

It is currently not possible to export this to a file, but as a work around, use “select all” to select the all rows and then “paste” into a text editor

#3

I have just added a new File->Export->Selection…
feature that can be used to export whatever is selected in the long read inspector to a file, it will available with the next update later this week

#4

Release 6_12_6 has this feature

#5

Thank you Daniel!

I will try this version as soon as possible.

CY

#6

Hi, Daniel:

It works with the new version. Thank you so much for the new feature!
May I suggest another possible feature for next version? On the table of the Long read inspector, maybe it will be worthy to put the identity% for the blast results correlated with the Assignment column (or the results with the highest coverage). It can be a useful feature for the users.

Thank you so much for developing this wonderful program!

Best Wishes,

CY

#7

Hi Daniel,

I managed to cut and paste my long read inspector data to notepad ++. I was wondering if you could explain what each number means? Matches is the number of alignments to the respective contig, but what does the bigger number mean?

Thanks! KV

read assignment mode = aligned bases

  • dolphinfeces.flye.medaka.consensus.blastx.rma6
  • Taxonomy
  • Autographiviridae [1,548] (what is this number??)
  • contig_101 [matches=7]
  • DATA
  • uncultured phage_MedDCM-OCT-S45-C18; score=127.0
  • Nonlabens phage P12024L; score=91.0
  • Nonlabens phage P12024S; score=91.0
  • Rhodobacter phage RcapMu; score=88.0
  • Synechococcus phage S-CAM4; score=86.0
  • Synechococcus phage ACG-2014j; score=86.0
  • Phage MedPE-SWcel-C56; score=69.0
  • contig_50 [matches=1]
  • DATA
  • uncultured phage_MedDCM-OCT-S45-C18; score=247.0
  • Myoviridae [1,266]
  • Podoviridae [582]
  • Salasmaviridae [2,190]
  • Siphoviridae [33,237]
  • Inoviridae [1,980]
  • Microviridae [14,990]
  • Parvoviridae [4,503]
  • Circoviridae [1,335]
  • unclassified RNA viruses ShiM-2016 [759]
  • Iridoviridae [897]
#8

The larger number in brackets is the “class size”. The interpretation depends on which “read assignment mode” is set. In your case, this is set to “aligned bases”. So, in your case, the number is the total number of aligned bases.

#9

r, Thank you. Is there a way to export total blast x hits (alignments) to different viral families?

#10

Hi Daniel,
Would one use the total number of aligned bases to see how much of a genome was recovered by X number of contigs?

I am wondering how I can use Megan to extract contigs for genome assembly? It is best to extract all the contigs that align to a particular virus family or genus, or species then download the reference genomes and run a genome alignment?

#11

You can also set the read assignment mode to “bases”, which counts the based assigned to a taxon, not just the aligned bases. We introduced the “number of aligned bases” for early versions of Nanopore sequencing, where reads sometimes appeared to contain large stretches of “garbage” bases… It seemed safer to only count bases that align to something…

I’m not sure I understand what you mean by extract contigs for assembly? Do you mean long reads rather than contigs? Or do you want to try to assemble the (already assembled) contigs? Either way, MEGAN allows you to select nodes in the taxonomy view and then save all assigned reads/contigs to a file. You can use %t and %i in the supplied file name to put things into files whose name contain the taxon name (place holder %t) and/or taxon id (place holder %i).

#12

Hi Daniel,

I mean can I export only the contigs from the viral families of interest if I want to do an alignment with a reference genome using bowtie (or some other alignment tool). Like if I have alot of alignments to one particular virus, I would want to extract those contigs and align it to a reference genome.

#13

Hi Daniel,

I figured out how to export the selected inspector viral families and I just changed the .txt to a .csv and that worked. Thanks!

#14

If you want to save the contigs assigned to a particular node, select the node in the main taxonomy viewer (or one of the other classification viewers) and then use the following menu item:

File->Extract Reads…

This will place all reads (or contigs) assigned to one or more selected nodes to text files. You can use place-holders %f, %t and %i in the specify file names to have reads to different files. The place holders are replaced by input file name, class name and class id, respectively.

#15

Thanks Daniel! I will try this out!