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Forum: Sample Prep / Library Generation 12-01-2019, 08:10 PM
Replies: 18
Views: 3,299
Posted By Meyana
I can't see why there should be any problem in...

I can't see why there should be any problem in doing the upper size selection now, I would just try and see how it sequences.

Hope it works.
Forum: Sample Prep / Library Generation 10-20-2019, 09:47 PM
Replies: 2
Views: 885
Posted By Meyana
I always use the NEBNext High-Fidelity 2 PCR...

I always use the NEBNext High-Fidelity 2 PCR Master Mix (New England Biolabs, cat. no. M0541) for PCR when making ATAC libraries, I find it much more reliable than the one in the Nextera prep kit.
...
Forum: Sample Prep / Library Generation 08-20-2019, 04:53 PM
Replies: 18
Views: 3,299
Posted By Meyana
I always do both upper and lower size selection...

I always do both upper and lower size selection using AMPure XP beads, I don't see a reason not to just do it right away (unless you are unfamiliar with bead cleanup and want to have a way to check...
Forum: Sample Prep / Library Generation 08-14-2019, 02:34 AM
Replies: 18
Views: 3,299
Posted By Meyana
I started out using the PCR mix in the Nextera...

I started out using the PCR mix in the Nextera kit for both PCR and qPCR and got little to no amplification. Switching all steps to NEB (as described in the Omni paper) got everything working...
Forum: Bioinformatics 08-05-2019, 06:50 PM
Replies: 3
Views: 601
Posted By Meyana
The time of run will depend on the read length. ...

The time of run will depend on the read length.

Check this link for run times for different read lengths:
https://www.illumina.com/systems/sequencing-platforms/miseq/specifications.html
Forum: Bioinformatics 08-04-2019, 08:56 PM
Replies: 0
Views: 514
Posted By Meyana
Pair-wise comparison of DNA sequences

Hi,
I'm hoping someone can help me with what I presume to be a simple task, but one I couldn't find a solution to myself :)

I have a table of DNA sequences with two columns, like this:

Seq1 ...
Forum: Bioinformatics 07-31-2019, 01:47 AM
Replies: 2
Views: 778
Posted By Meyana
Looks like something you could quite easily make...

Looks like something you could quite easily make using ggplot2 package in R.
Tons of guides floating around on that.

I don't know Infopath.
Forum: Introductions 07-10-2019, 05:25 PM
Replies: 1
Views: 779
Posted By Meyana
If you are using different cell lines you are...

If you are using different cell lines you are comparing just that, cell lines. Not patient-derived samples. You cannot infer that their "diversity" will mimic that of patients-derived cells, nor can...
Forum: Sample Prep / Library Generation 03-26-2019, 10:39 PM
Replies: 5
Views: 3,450
Posted By Meyana
I have seen this on FACS'ed neuronal nuclei....

I have seen this on FACS'ed neuronal nuclei. Switching to the Omni-ATAC protocol (and handling the procedure a few times) solved everything and I now reliably get good looking BA tracks.
When...
Forum: Bioinformatics 03-25-2019, 04:58 PM
Replies: 8
Views: 1,668
Posted By Meyana
Great, happy to see it working for you! :) ...

Great, happy to see it working for you! :)

In addition to the UpSetR package, there's also the SuperExactTest package, which you may also find interesting (though the graphical output is not the...
Forum: Bioinformatics 03-24-2019, 05:37 PM
Replies: 8
Views: 1,668
Posted By Meyana
Your code works fine on my data. Could you post...

Your code works fine on my data.
Could you post a snippet of your data?
Forum: Bioinformatics 03-22-2019, 02:13 AM
Replies: 8
Views: 1,668
Posted By Meyana
My data1/data2/data3 are just vectors of the...

My data1/data2/data3 are just vectors of the observations, which I then store in the list listInput, nothing special. The data observations themselves can have any format, mine look something like...
Forum: Bioinformatics 03-21-2019, 10:57 PM
Replies: 8
Views: 1,668
Posted By Meyana
I run UpSetR by inputting individual sets as a...

I run UpSetR by inputting individual sets as a list and then the program calculates overlap itself (I am not aware whether it allows you to "manually" input the overlaps, never tried that).

#make...
Forum: Bioinformatics 01-28-2019, 08:52 PM
Replies: 2
Views: 916
Posted By Meyana
I have been really pleased with using the variant...

I have been really pleased with using the variant caller that is a part of the BBTools package for rare variants in mitochondrial DNA. ...
Forum: Sample Prep / Library Generation 12-13-2018, 04:38 PM
Replies: 18
Views: 3,299
Posted By Meyana
I have seen the same thing repeatedly with FACS...

I have seen the same thing repeatedly with FACS sorted nuclei isolated from frozen tissue, hoping someone has an idea on how to optimize...
Forum: Bioinformatics 10-04-2018, 05:21 PM
Replies: 3
Views: 806
Posted By Meyana
Please refer to the bbtools manual here: ...

Please refer to the bbtools manual here:
https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/

And the callvariants page here:...
Forum: Bioinformatics 10-03-2018, 12:23 AM
Replies: 3
Views: 806
Posted By Meyana
Might be a limit to the indel caller. I'd...

Might be a limit to the indel caller.

I'd suggest using bbmap for mapping and CallVariants (also in the BBtools suite), I'm successfully calling long (>10kb) indels using 150bp paired end reads...
Forum: RNA Sequencing 09-25-2018, 12:04 AM
Replies: 2
Views: 2,159
Posted By Meyana
I'm using the NuGEN Ovation Solo library prep kit...

I'm using the NuGEN Ovation Solo library prep kit (https://www.nugen.com/products/ovation-solo-rna-seq-system), it's for low RNA input. They have this similar one...
Forum: Bioinformatics 08-14-2018, 10:05 PM
Replies: 676
Views: 176,571
Posted By Meyana
Hi, Hoping somebody can help me with this. ...

Hi,
Hoping somebody can help me with this.

I used BBMap and now I would like to extract the reads from by .bam file that are split (/chimeric?) ie. reads that indicate a deletion.

I tried to...
Forum: Sample Prep / Library Generation 06-18-2018, 06:54 PM
Replies: 3
Views: 1,318
Posted By Meyana
I agree on just incubating longer - I put my...

I agree on just incubating longer - I put my samples on the thermomixer with intermittent mixing until they dissolve. It works fine :)
Forum: Bioinformatics 05-14-2018, 08:46 PM
Replies: 676
Views: 176,571
Posted By Meyana
Dear Brian, I am using bbmap for mapping and...

Dear Brian,

I am using bbmap for mapping and callvariants.sh for variant calling on PE Illumina reads.
I am comparing two mice strains. I am therefore downsampling my .sam files to have the same...
Forum: Bioinformatics 05-06-2018, 04:59 PM
Replies: 2
Views: 790
Posted By Meyana
Anyone that might know how to do something like...

Anyone that might know how to do something like this? :)
Forum: Bioinformatics 04-26-2018, 11:14 PM
Replies: 2
Views: 790
Posted By Meyana
Cool Add user specified reads to fastq to validate analysis method?

Hi,

I am analyzing mtDNA and am looking for indels, especially I am hoping to catch some large deletions.
I have performed 150bp PE on MiSeq using NexteraXT library prep.

Using different...
Forum: Illumina/Solexa 12-14-2017, 08:23 PM
Replies: 15
Views: 2,805
Posted By Meyana
I just finished the run of my first 24 samples on...

I just finished the run of my first 24 samples on the MiSeq. Thank you all for your great input!

Unfortunately, it was really under clustered, with only 305K/mm2. 88.2% of clusters passed...
Forum: Illumina/Solexa 12-07-2017, 08:41 PM
Replies: 15
Views: 2,805
Posted By Meyana
Great to know. I was just about to ask how to...

Great to know. I was just about to ask how to choose between 6, 8, and 10pM, I haven't seen any info or guidelines on how you know what you should do. Could you add any further information for my...
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