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Forum: Bioinformatics 07-05-2016, 12:32 PM
Replies: 0
Views: 850
Posted By exo
similarity plots using R

Hi all!

I just wanted to see whether someone can tell me whether there is an R package that does sequence similarity plotting like SimPlot and DnaSP. Those softwares work great but the quality of...
Forum: Bioinformatics 06-12-2016, 06:32 AM
Replies: 5
Views: 2,037
Posted By exo
Counting specific sequence stretches in fastq files

Hey all,

For a while ive been trying to find a way how to count specific sequence stretches directly from fastq files. For example i would like to see how many reads contain the following...
Forum: Bioinformatics 01-03-2016, 08:39 AM
Replies: 2
Views: 1,394
Posted By exo
That looks like an interesting package! Thank...

That looks like an interesting package!
Thank you!
Forum: Bioinformatics 01-02-2016, 01:34 AM
Replies: 2
Views: 1,394
Posted By exo
plotting SNP data using ggplot2

Hi all,

First off, i wish you all a happy new year.

I have a question regarding plotting SNP data using the scatter function in ggplot2. I am plotting data from 5 different timepoints using the...
Forum: Illumina/Solexa 05-13-2015, 04:17 AM
Replies: 7
Views: 5,028
Posted By exo
Have you seen better results when you changed the...

Have you seen better results when you changed the polymerase?
Forum: Sample Prep / Library Generation 04-15-2015, 01:39 AM
Replies: 4
Views: 1,455
Posted By exo
modification of ScriptSeq-RNA v2 protocol to accommodate v3 chemistry

Dear all,

Just wanted to share with you some possible modifications i will be implementing in the ScriptSeq RNA v2 protocol for sequencing using the V3 chemistry.

1- I was thinking to reduce...
Forum: RNA Sequencing 04-10-2015, 01:28 AM
Replies: 2
Views: 1,503
Posted By exo
Thank you for the reply! Indeed tweaking the...

Thank you for the reply!

Indeed tweaking the bead to sample ratio will only affect the final library size rather than the quality of the library itself.

I think the problem in those libraries...
Forum: RNA Sequencing 04-08-2015, 09:37 AM
Replies: 2
Views: 1,503
Posted By exo
Trouble shooting a low quality RNA-seq run/modofications

Dear All,

I've recently started performing RNA-seq experiments to sequence whole viral genomes. I started with using the Script-Seq kit (originally sold by epicenter). I start the protocol with...
Forum: Bioinformatics 03-02-2015, 12:27 AM
Replies: 2
Views: 841
Posted By exo
Thank you! But this won't show me the low...

Thank you! But this won't show me the low variants, that are not present in the consensus sequence.
I was looking to track within host evolution and whether that has any unique mutational signatures.
Forum: Bioinformatics 02-26-2015, 08:01 AM
Replies: 2
Views: 841
Posted By exo
SNPs and their neighboring nucleotides

Hey,

I was wondering whether anyone out there has a script or a software capable of extracting SNPs with its neighboring bases from read mapping.

What i am interested in is to check for...
Forum: Bioinformatics 11-04-2014, 06:16 AM
Replies: 2
Views: 1,772
Posted By exo
Wow ok, that worked thank you! Apparently -lz was...

Wow ok, that worked thank you! Apparently -lz was missing from the Makefile adding your suggestion while running the "./configure" command fixed it!

Thank you!
Forum: Bioinformatics 11-04-2014, 05:25 AM
Replies: 2
Views: 1,772
Posted By exo
GapFiller compiling problem

Hey!

For the last couple of days I've been trying to install GapFiller on linux. Sadly, i failed several times. After I ./configure; make i end up with the following error:
...
Forum: Sample Prep / Library Generation 03-13-2014, 12:34 AM
Replies: 3
Views: 11,530
Posted By exo
Weird bioanalyzer results

Hey all,

Yesterday, for the first time ever i was about to slam my head into the bioanalyzer. I ran 8 samples prepared with nexteraxt protocol after pcr cleanup and size selection using 29ÁL of...
Forum: Sample Prep / Library Generation 02-21-2014, 04:23 AM
Replies: 9
Views: 2,546
Posted By exo
Alright perfect, and that would not interfere...

Alright perfect, and that would not interfere with the adaptor trimming option on the MiSeq right? Assuming that i select "nextera" in my sample sheet.
Forum: Sample Prep / Library Generation 02-20-2014, 07:04 AM
Replies: 9
Views: 2,546
Posted By exo
Alright, perfect thanks for the input! :)

Alright, perfect thanks for the input! :)
Forum: Sample Prep / Library Generation 02-19-2014, 12:05 AM
Replies: 9
Views: 2,546
Posted By exo
Yea, I also skip the beads normalization step in...

Yea, I also skip the beads normalization step in the NexteraXT protocol. But would pooling of library A (done with Nextera) and library B (done with NexteraXT) on the same seqeuncing run effect the...
Forum: Sample Prep / Library Generation 02-18-2014, 06:33 AM
Replies: 9
Views: 2,546
Posted By exo
Pooling of Nextera and NexteraXT libraries

Hey all,

So i was thinking, can you actually pool both nextera and nexteraXT prepd libraries on the same cycling run?
I mean theoretically, this should be possible since both kits use the same...
Forum: Illumina/Solexa 12-02-2013, 03:47 AM
Replies: 15
Views: 17,049
Posted By exo
Well, previously i was clustering at around...

Well, previously i was clustering at around 800k/mm2. Thats why i had to increase my input concentration to hit the 1200-1400 range.
Can you say what was your cluster density with v2 and v3 using...
Forum: Illumina/Solexa 11-29-2013, 05:13 AM
Replies: 12
Views: 12,639
Posted By exo
I have a relatively dumb question. Doesnt the...

I have a relatively dumb question. Doesnt the MiSeq have an integrated adaptor trimming option?
Forum: Illumina/Solexa 11-29-2013, 05:10 AM
Replies: 15
Views: 17,049
Posted By exo
Sorry just noticed this thread was active! So, I...

Sorry just noticed this thread was active! So, I actually managed to sequence using the v3 chemistry last month. I just estimated that 20pM would cluster at around 1200-1400 - since previously, we...
Forum: Sample Prep / Library Generation 09-17-2013, 07:33 AM
Replies: 3
Views: 2,110
Posted By exo
Hi, I really doubt pcring out 20kb regions...

Hi,

I really doubt pcring out 20kb regions is optimal. Well, actually i doubt it will work that way at all - but thats just me. You will either have to make smaller amplicons, which will be...
Forum: Illumina/Solexa 09-17-2013, 07:30 AM
Replies: 15
Views: 17,049
Posted By exo
MiSeq Reagent kit v3

Hey all,

Anyone has tried using the MiSeq v3 chemistry yet? We just bought a kit and im planning a run next week, and i wanted to see what would you guys recommend concerning lib size...
Forum: Bioinformatics 09-09-2013, 12:05 AM
Replies: 4
Views: 4,142
Posted By exo
Perfect, thanks for the input!

Perfect, thanks for the input!
Forum: Bioinformatics 09-06-2013, 01:17 AM
Replies: 4
Views: 4,142
Posted By exo
Visualizing SNPs throughout a circular genome

Hi there,

I recently sequenced 8 small viral genomes, and when compared to the only publicly available reference more than 250 SNPs were detected. For visualization, i thought it might be a good...
Forum: Sample Prep / Library Generation 06-05-2013, 04:28 AM
Replies: 2
Views: 2,009
Posted By exo
Thank you for your reply! I ran 1:3 dilution...

Thank you for your reply!
I ran 1:3 dilution aliquotes of my libraries on a HS DNA Chip, before and after fragmentation. Seems like i have fragments ranging from 350bp to 1500bp, with a peak at 1kb...
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