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Forum: Bioinformatics 11-11-2016, 09:26 AM
Replies: 0
Views: 992
Posted By Lovro
genomicAlignments package in R

Hi,

using:
flagL <- scanBamFlag(isDuplicate=FALSE, isNotPassingQualityControls=FALSE)
ParamL <- ScanBamParam(flag = flagL, what="seq")
BAM <- readGAlignmentPairs(file.bam,use.names = T, param =...
Forum: Sample Prep / Library Generation 09-13-2016, 06:15 AM
Replies: 23
Views: 17,216
Posted By Lovro
They are from Nextera exome kit, not generic...

They are from Nextera exome kit, not generic nextera.
http://www.illumina.com/products/nextera-rapid-capture-exome-kits.html

tnx for all the info!
Forum: Sample Prep / Library Generation 09-13-2016, 03:14 AM
Replies: 23
Views: 17,216
Posted By Lovro
Thank you for the link. I will use the beads...

Thank you for the link.

I will use the beads that come with Nextera kits:

https://i.imgsafe.org/7ce56ea725.jpg

Are there any specificities on them I should know about ?

In regard to the...
Forum: Sample Prep / Library Generation 09-09-2016, 10:28 AM
Replies: 13
Views: 3,179
Posted By Lovro
I'm sorry, but I was misinformed. Indeed the...

I'm sorry, but I was misinformed.

Indeed the libraries are 1000bp long on average, but after sequencing these are the results:

https://i.imgsafe.org/2f079678cf.png

Yes, I meant normal...
Forum: Sample Prep / Library Generation 09-09-2016, 10:18 AM
Replies: 23
Views: 17,216
Posted By Lovro
I was under impression that bead size selection...

I was under impression that bead size selection is one sided and different concentrations of SPB bind DNA from certain length upwards. Setting the threshold at lower lengths would therefore result in...
Forum: Sample Prep / Library Generation 09-08-2016, 05:49 AM
Replies: 23
Views: 17,216
Posted By Lovro
Thank you! Almost forgot about the blockers...

Thank you!
Almost forgot about the blockers used in enrichment.

By one sided you mean I have to get rid only of the shorter fragments? With 0.45-0.48x AMPure beads you suggest I keep the beads or...
Forum: Sample Prep / Library Generation 09-08-2016, 04:31 AM
Replies: 13
Views: 3,179
Posted By Lovro
1000bp insert size with Illumina TruSeq DNA PCR-Free Library prep kit

Hi!

I'm considering modifying Illumina TruSeq DNA PCR-Free Library prep kit protocol to produce 1000bp insert size libraries for sequencing on MySeq.

The reason is that the libraries produced...
Forum: Sample Prep / Library Generation 09-08-2016, 02:46 AM
Replies: 23
Views: 17,216
Posted By Lovro
Thank you for all the info and this nice summary....

Thank you for all the info and this nice summary.
I was wondering if you guys have any advice on eliminating large fragments. The step is included in TruSeq DNA PCR-Free library prep from Illumina....
Forum: Illumina/Solexa 09-01-2016, 09:25 AM
Replies: 6
Views: 2,656
Posted By Lovro
Thank you very much. I will mention this to their...

Thank you very much. I will mention this to their representative.
Forum: Illumina/Solexa 08-30-2016, 05:37 AM
Replies: 6
Views: 2,656
Posted By Lovro
Hi, thanks for the answers. We have considered...

Hi, thanks for the answers.
We have considered the latter.
However, I was more interested in finding out the meaning of the error code.

We had a hardware problem with a moveable mirror part...
Forum: Illumina/Solexa 08-25-2016, 02:45 AM
Replies: 6
Views: 2,656
Posted By Lovro
myseq error "waiting for FPGA command CAMDBLSNAP"

Hi,

I would appreciate any help in regard to the following MySeq error:

Timeout of 70.000 seconds exceeded while waiting for FPGA command "CAMDBLSNAP 390 390 188 188 34390 150" to complete.
...
Forum: Illumina/Solexa 07-06-2016, 02:10 PM
Replies: 8
Views: 31,760
Posted By Lovro
I was working on a virtual machine and had only...

I was working on a virtual machine and had only cca 100gb left on the hdd. I have 2 WGS fastq.gz with 50gb each... I solved the problem by allocating extra hdd space to the virtual machine, but I...
Forum: Illumina/Solexa 07-06-2016, 03:15 AM
Replies: 8
Views: 31,760
Posted By Lovro
This preserves the original files. Can I rather...

This preserves the original files. Can I rather append the second file to the first, to conserve disk space ?
Forum: Illumina/Solexa 06-22-2016, 01:36 AM
Replies: 3
Views: 2,498
Posted By Lovro
Thank you both for your answers and a link! As...

Thank you both for your answers and a link!
As long as it can be done I will try it. I will get back with more questions when I get my reagents and prepare and enrich the libraries.

Thank you!
Forum: Illumina/Solexa 06-20-2016, 03:32 AM
Replies: 3
Views: 2,498
Posted By Lovro
Truseq libray spike-in into Nextera library run

Hi.

In our lab we routinly perform exome sequencing with Nextera kits on Mi/HiSeq platforms.
In my experiment I want to sequence libraries made with Truseq DNA PCR-free LT kit and enriched with...
Forum: Sample Prep / Library Generation 06-08-2016, 05:28 AM
Replies: 0
Views: 1,665
Posted By Lovro
which library kit; are adapters on Illumina PCR free LT kit biotinylated ?

Hi,
I would like to prepare an enriched (custom IDT lockdown probes) NGS (Illumina platform) library that has a PCR step as late as possible in the protocol - I want to bisulfite treat the already...
Forum: Illumina/Solexa 03-23-2016, 05:03 AM
Replies: 5
Views: 6,692
Posted By Lovro
Hi. I would like to bisulfite sequence...

Hi.

I would like to bisulfite sequence (Illumina platform) selected loci on human genome.
I have ordered custom hybridization probes from IDT in order to enrich the human DNA. I was under...
Forum: Bioinformatics 12-03-2015, 03:41 AM
Replies: 17
Views: 44,756
Posted By Lovro
i have the same problem... this is from the...

i have the same problem...

this is from the man samtools:
o Import SAM to BAM when @SQ lines are present in the header:

samtools view -bS aln.sam > aln.bam

If @SQ lines...
Forum: Bioinformatics 05-13-2015, 03:01 AM
Replies: 2
Views: 1,376
Posted By Lovro
how have you fixed it ?

Hello,

I'm getting the same error when trying to "make" trinity v 2012-06-08 on ubuntu. I was wondering how did you solve the issue...

I'm trying to use this version with virusfinder2.0, since...
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