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Forum: Illumina/Solexa 04-10-2019, 08:29 AM
Replies: 16
Views: 2,451
Posted By apredeus
Hello, I don't quite remember since it was...

Hello,

I don't quite remember since it was a long time ago :) but I'm pretty sure that the reason this happened is due to Illumina software being confused by the adapter and short read sequence....
Forum: Oxford Nanopore 09-28-2018, 03:53 AM
Replies: 14
Views: 6,259
Posted By apredeus
We had it working with non-SSD drives without any...

We had it working with non-SSD drives without any issue, as long as you don't basecall at the same time. I don't know if that's going to change with the new MinKNOW or newer flow cells, since the...
Forum: Bioinformatics 01-19-2018, 12:05 PM
Replies: 15
Views: 2,766
Posted By apredeus
Thank you for the suggestions.

Thank you for the suggestions.
Forum: Bioinformatics 01-19-2018, 11:37 AM
Replies: 15
Views: 2,766
Posted By apredeus
I know, that's why I was surprised - two separate...

I know, that's why I was surprised - two separate installations, two different errors!



So, in the instance when it appears to install without any errors, bamCoverage produces the following...
Forum: Bioinformatics 01-19-2018, 10:53 AM
Replies: 15
Views: 2,766
Posted By apredeus
deepTools actually prove pretty hard to get to...

deepTools actually prove pretty hard to get to work - one conda environment and pip they fail to install with separate errors, and another conda environment they seem to install fine, but throw a...
Forum: Bioinformatics 11-08-2017, 04:27 AM
Replies: 2
Views: 1,565
Posted By apredeus
There is a tool from Schatz lab called NanoCORR:...

There is a tool from Schatz lab called NanoCORR: http://schatzlab.cshl.edu/data/nanocorr/

I don't think it's used much though. Also, as far as I know, nanopolish is the only tool that uses fast5...
Forum: Bioinformatics 11-04-2017, 10:15 AM
Replies: 3
Views: 4,409
Posted By apredeus
Do you guys know the version history for Illumina...

Do you guys know the version history for Illumina exome designs? They don't post them explicitly as Agilent or Roche, and that's too bad. I do think that the designs have changed - earlier papers...
Forum: Oxford Nanopore 11-03-2017, 05:26 AM
Replies: 1
Views: 3,171
Posted By apredeus
It's probably better to ask this question on...

It's probably better to ask this question on nanopore forums, you should have the access by now - they have more users and can give more detailed feedback.

I've seen people run it without any...
Forum: Oxford Nanopore 11-03-2017, 04:39 AM
Replies: 7
Views: 4,521
Posted By apredeus
If you got plenty of computational resources, run...

If you got plenty of computational resources, run several assemblies and then see which one does best. If you are moderately successful with your 1D runs, you'll generate about 10 Gb of data from two...
Forum: Oxford Nanopore 11-03-2017, 04:30 AM
Replies: 4
Views: 4,294
Posted By apredeus
I've used minimap2 from Heng Li to map the long...

I've used minimap2 from Heng Li to map the long reads before polishing - it's much faster and gives similar results. Bwa with ont2d works as well, just somewhat slower.

Nanopolish has changed...
Forum: Illumina/Solexa 06-09-2017, 07:08 AM
Replies: 23
Views: 6,974
Posted By apredeus
Thank you very much! This is extremely useful.

Thank you very much! This is extremely useful.
Forum: Illumina/Solexa 06-07-2017, 07:53 AM
Replies: 23
Views: 6,974
Posted By apredeus
Along the same lines, and rather than multiplying...

Along the same lines, and rather than multiplying threads - are there any comprehensive reviews of all the indexing strategies available for Illumina?

And what would be a most reliable indexing...
Forum: Oxford Nanopore 06-07-2017, 07:26 AM
Replies: 32
Views: 20,332
Posted By apredeus
Thank you! Can anybody comment on how...

Thank you!

Can anybody comment on how reproducible are the methods used to measure the DNA concentration for long DNA fragments? I can't seem to get consistent results.
Forum: Oxford Nanopore 05-30-2017, 02:36 PM
Replies: 14
Views: 6,259
Posted By apredeus
This counts as a newbie question, I guess, so I...

This counts as a newbie question, I guess, so I won't multiply threads.

1) It states that it is "recommended" to run the phage experiment, and to officially submit the results back to Oxford...
Forum: Oxford Nanopore 05-30-2017, 02:19 PM
Replies: 32
Views: 20,332
Posted By apredeus
any of the experienced users could help? I've...

any of the experienced users could help? I've used a standard RNAse-proteinase digestion method for our bacteria, but it seems like it was too sturdy, and RNAse got destroyed before most cells were...
Forum: Bioinformatics 04-29-2017, 04:36 PM
Replies: 189
Views: 65,576
Posted By apredeus
You are right, thank you! The message confused me...

You are right, thank you! The message confused me as well.
Forum: Bioinformatics 04-29-2017, 03:46 PM
Replies: 189
Views: 65,576
Posted By apredeus
Note that the adapter sequences used for...

Note that the adapter sequences used for palindrome mode are the reverse complements of the sequences used in simple mode.

Ok, I understand now. And it's the rev-comp of /2 that is present in read...
Forum: Bioinformatics 04-29-2017, 01:15 PM
Replies: 189
Views: 65,576
Posted By apredeus
I've also found a strange issue with the...

I've also found a strange issue with the "keepBothEnds" option.

In the example I have described two posts above (but with bigger files, 25K reads each), the following command

java -jar $JAR PE...
Forum: Bioinformatics 04-29-2017, 01:05 PM
Replies: 189
Views: 65,576
Posted By apredeus
Dear Tony, few small suggestions that can...

Dear Tony,

few small suggestions that can make the program a lot easier to use -

1) just require 1 tag/prefix for the output, and use that to construct the output file names. Four file names...
Forum: Bioinformatics 04-29-2017, 12:58 PM
Replies: 189
Views: 65,576
Posted By apredeus
Hello Brian, did you figure out what was...

Hello Brian,

did you figure out what was the issue? I'm perplexed - I wanted to use Trimmomatic and BBduk and compare the results, however, Trimmomatic just would not remove the adapter that is...
Forum: Oxford Nanopore 01-04-2017, 07:16 AM
Replies: 5
Views: 4,173
Posted By apredeus
Thank you for the answers, I appreciate it. ...

Thank you for the answers, I appreciate it.

I'm checking the storage conditions and it seems like currently there are no kits that could be stored at RT, rapid kit included. Is that right? So do...
Forum: Oxford Nanopore 01-04-2017, 07:10 AM
Replies: 32
Views: 20,332
Posted By apredeus
Thank you, as soon as we do the run I'll...

Thank you, as soon as we do the run I'll definitely do that.
Forum: Oxford Nanopore 12-30-2016, 10:22 AM
Replies: 32
Views: 20,332
Posted By apredeus
Excellent, thank you for the insight, I...

Excellent, thank you for the insight, I appreciate all the info.

So if the method doesn't work well for R9.4, what would you recommend? A different kit?
Forum: Oxford Nanopore 12-28-2016, 11:23 AM
Replies: 5
Views: 4,173
Posted By apredeus
Thank you. So for 1D regular genomic DNA you need...

Thank you. So for 1D regular genomic DNA you need this, right?

https://store.nanoporetech.com/catalog/product/view/id/144/s/native-barcoding-kit-1d/category/17/

Do you have to store both the...
Forum: Oxford Nanopore 12-27-2016, 02:39 PM
Replies: 32
Views: 20,332
Posted By apredeus
This is for 2D protocol, right? Since I figured...

This is for 2D protocol, right? Since I figured you don't need Streptavidin beads for the 1D.

Do you have the detailed protocol for 1D? Would/did you change anything for the new flowcell (R9.4)?...
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