[mira_talk] Re: MIRA run failing due to megahubs
- From: "Offord, Victoria" <vofford@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 25 Jun 2014 16:08:52 +0000
Hi Martin,
Wow, thanks for the super speedy response!!!
Have run a couple of the repeats through BLAST and it seems some match to rRNA.
Am also seeing a lot of polyA-tails in there too.
I ran all of the reads through seqclean and assumed that this would fix the
above. In hindsight, I probably should have been a bit more ruthless.
Any advice on how to clean up the dataset a bit more or should I just drop the
reads?
Be kind, I'm a transcriptome assembling newbie! ;)
Thanks in advance!
Victoria
-----Original Message-----
From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On
Behalf Of Martin MOKREJŠ
Sent: 25 June 2014 17:02
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: MIRA run failing due to megahubs
Hi Victoria,
you have to look into the reads listed in *megahubs* file placed in
MergedAssembly/MergedAssembly_d_tmp/
subdirectory. Most likely you have too many polyA-tails in your data or rRNA
contamination or unremoved adapters/MIDs. Or simple crap like [CA]n repeats
causes that (sometimes they are authentic, sometimes not, in either case hard
to be useful). Provided it is so few reads, just drop them from your input
dataset.
Transcriptomic datasets need proper adapter removal and trimming ... see
below my signature. ;) Or maybe you get back to me later once you get 40kb long
contigs in your assemblies ... :)) Martin
Offord, Victoria wrote:
> Hi,
>
> My MIRA run on a parasite transcriptome keeps ending with:
>
> You have 0.1052271917% of your reads as megahubs.
> You have set a maximum allowed ratio of: 0.0000000000
--
Martin Mokrejs, Ph.D.
454 / IonTorrent / Evrogen MINT / Clontech SMART adapter/artifact removal (...
too many protocols to name here)
http://www.bioinformatics.cz/software/supported-protocols/
--
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