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Forum: Bioinformatics 03-08-2018, 09:56 AM
Replies: 2
Views: 1,126
Posted By cstack
Just so we are using the same terminology: An...

Just so we are using the same terminology: An assembly gap is typically represented by a series of N's connecting two contigs; the product of 2+ contigs connected by gaps is referred to as a...
Forum: Bioinformatics 03-08-2018, 09:39 AM
Replies: 2
Views: 1,659
Posted By cstack
I am not 100% clear on what additional data you...

I am not 100% clear on what additional data you are trying to pull out from the blastn output.

Could you post a sample of the blastn output, and maybe a rough schematic of what you wish the them...
Forum: Bioinformatics 11-06-2017, 11:28 AM
Replies: 3
Views: 879
Posted By cstack
It seems there are specific read alignments that...

It seems there are specific read alignments that are causing the failures. You could confirm this by using taking one of the .bam's that failed, use different random seeds w/ a small sample...
Forum: Bioinformatics 11-06-2017, 07:14 AM
Replies: 2
Views: 1,632
Posted By cstack
I guess you could try an all-vs-all mapping...

I guess you could try an all-vs-all mapping (skipping self-mapping) -- I think that graphmap (https://github.com/isovic/graphmap) and minialign (https://github.com/ocxtal/minialign) can do this and...
Forum: Oxford Nanopore 11-03-2017, 06:45 PM
Replies: 4
Views: 4,569
Posted By cstack
Like an earlier user mentioned, the initial...

Like an earlier user mentioned, the initial indexing step links each read in the fastq file with a fast5 record.

Prior to basecalling with albacore 2, you would use nanopolish extract to make...
Forum: Oxford Nanopore 08-11-2017, 07:14 AM
Replies: 7
Views: 4,822
Posted By cstack
We work on a plant species that is difficult to...

We work on a plant species that is difficult to get DNA from, and from our first few flowcells we were getting approx. 3-5Gbp of 1d reads (using 9.4 chem w/ the standard ligation kit). If you get...
Forum: Oxford Nanopore 08-10-2017, 02:18 PM
Replies: 7
Views: 4,822
Posted By cstack
Maybe. What is your Illumina coverage? There...

Maybe. What is your Illumina coverage? There are a few scaffolders that would seem to work for that sort of thing. This manuscript (https://www.nature.com/articles/s41598-017-03996-z) has good...
Forum: Bioinformatics 08-10-2017, 10:14 AM
Replies: 1
Views: 875
Posted By cstack
bbduk.sh masking shorter than k-mer size

I've come across a situation using bbduk to mask the k-mers from one genome assembly in another where the resulting number of masked bases is some sequences is shorter than the k value.

I am...
Forum: Pacific Biosciences 05-05-2017, 09:02 AM
Replies: 9
Views: 2,373
Posted By cstack
I ran CircularConsensus (ConsensusTools...

I ran CircularConsensus (ConsensusTools v2.3.0.149240) using these options:

ConsensusTools.sh CircularConsensus -n 16 \
--logFile=test_ccs.log \
--minFullPasses 0 --minPredictedAccuracy 0 \...
Forum: Pacific Biosciences 05-04-2017, 02:48 PM
Replies: 9
Views: 2,373
Posted By cstack
Thanks much for the reply. I tried running...

Thanks much for the reply. I tried running CircularConsensus on a single bax.h5 file, and I see what you mean about reduced read lengths.



I'll have a look through the PBjelly files and...
Forum: Pacific Biosciences 05-04-2017, 02:28 PM
Replies: 9
Views: 2,373
Posted By cstack
Thanks much for the reply. When you run...

Thanks much for the reply. When you run CircularConsensus, what quality threshold (or paramaters) do you typically use?
Forum: Pacific Biosciences 05-03-2017, 11:31 AM
Replies: 9
Views: 2,373
Posted By cstack
Is there any reason not to run RS_ReadsOfInsert?

I've included some background info after the questions, which are first in cases of TL;DR

Questions:
1. Is it generally a best-practice to run CircularConsensus on SMRT cell DNAseq data before...
Forum: Pacific Biosciences 05-03-2017, 08:18 AM
Replies: 8
Views: 3,460
Posted By cstack
Could these be true repetitive sequence? They...

Could these be true repetitive sequence? They might occur at the ends of scaffolds because it is difficult to assembly long stretches of repeats.



I have had the same thing happen recently...
Forum: Pacific Biosciences 05-03-2017, 08:01 AM
Replies: 4
Views: 1,771
Posted By cstack
I've run SMRT portal / tools (~ v2.3.0) on ubuntu...

I've run SMRT portal / tools (~ v2.3.0) on ubuntu 14.04 and not run in to any issues
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