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Forum: Illumina/Solexa 05-15-2019, 11:47 PM
Replies: 10
Views: 10,052
Posted By thiNGS
Hi! Yes it did work

Hi! Yes it did work
Forum: Sample Prep / Library Generation 04-05-2019, 07:48 AM
Replies: 17
Views: 8,279
Posted By thiNGS
Hi all. On a different note...I do not really...

Hi all. On a different note...I do not really understand how one is supposed to combine the N7 and S5 primers in the QIAseq Targeted DNA Panel. Do they have to be combined in a TruSeq-like fashion?...
Forum: Sample Prep / Library Generation 02-14-2019, 10:43 AM
Replies: 0
Views: 782
Posted By thiNGS
Inhibitors of DNA-magnetic beads binding

Hi all! I am trying to optimize cfDNA extraction testing different kits with commercial samples (artificial plasma). For some reason one set of samples does not work well with the magnetic beads kit....
Forum: RNA Sequencing 07-19-2018, 06:06 AM
Replies: 1
Views: 1,250
Posted By thiNGS
stabilize the RNA expression profile upon harvesting samples

Hi all. I am designing an experiment for RNAseq. I start treating my cells with a compound (or DMSO in the control) and collect samples at different timepoints. My question is: when I harvest the...
Forum: Illumina/Solexa 04-24-2018, 05:46 AM
Replies: 10
Views: 10,052
Posted By thiNGS
I suppose it will work with nextseq cartridges as...

I suppose it will work with nextseq cartridges as well? I accidentally thawed the wrong one and refroze it. Now I would like to use it hoping it will work. Anyone has tried before?
Forum: Illumina/Solexa 03-09-2018, 05:08 AM
Replies: 1
Views: 1,107
Posted By thiNGS
Talking bacterial RNAseq using TruSeq Lib prep

Hi all. I am in the process of starting RNAseq from bacterial samples and I am trying to identify the best strategy to do it. Given that bacterial RNA is not poly-adenylated, a random hexamer-based...
Forum: Illumina/Solexa 02-22-2018, 01:51 PM
Replies: 1
Views: 1,115
Posted By thiNGS
Update: I can't see any phix data either although...

Update: I can't see any phix data either although the library has been spiked in with a phix I used last week. It seems like phix has not been sequenced at all. Any thoughts? I am really confused,...
Forum: Illumina/Solexa 02-22-2018, 12:39 PM
Replies: 1
Views: 1,115
Posted By thiNGS
Nexseq run - very low density but good intensity

Hi all. I am running some samples on the nextseq and I have seen that after cycle 5 the intensity drops dramatically. At cycle 1 intensity was alright but then it massively goes down. The cluster...
Forum: Illumina/Solexa 02-17-2018, 09:15 AM
Replies: 5
Views: 1,840
Posted By thiNGS
Issue solved. There was a network failure so I...

Issue solved. There was a network failure so I requeued the analysis and now it's fine!!
Forum: Illumina/Solexa 02-17-2018, 07:44 AM
Replies: 5
Views: 1,840
Posted By thiNGS
Thank you jdk787. I have double checked the...

Thank you jdk787. I have double checked the sample sheet and this is fine. I can't see any error log file, could you please remind me where to look for it please?
Forum: Illumina/Solexa 02-17-2018, 05:45 AM
Replies: 5
Views: 1,840
Posted By thiNGS
I use basespace to monitor the run status...

I use basespace to monitor the run status remotely and also to download the fastq file because the nextseq machine is shared with other people so we use it just to set up the sequencing. I just don't...
Forum: Illumina/Solexa 02-17-2018, 03:12 AM
Replies: 5
Views: 1,840
Posted By thiNGS
Troubleshooting: Nexseq run completed but status is "failed"

Hi everyone. I prepped some samples with Nextera xt kit and run them on the next seq. I monitored the run and everything was fine until the uploading step. I can see cluster density, %pf and %q30,...
Forum: Ion Torrent 02-14-2018, 08:25 AM
Replies: 1
Views: 3,148
Posted By thiNGS
Storage of amplified library

Hello. I am using the Thermo Scientific™ MuSeek Library Preparation Kit for Ion Torrent™ and I have performed fragmentation, purification and adaptor+barcode ligation. Can I store the barcoded,...
Forum: Illumina/Solexa 02-02-2018, 02:54 AM
Replies: 6
Views: 1,949
Posted By thiNGS
Nextera XT for WGS of bacteria

Hello. I am using Nextera XT to do whole genome sequencing of bacteria grown in stress conditions/high concentrations of antibiotics. What I found is, even if I follow the protocol correctly, I end...
Forum: Illumina/Solexa 01-18-2018, 10:42 AM
Replies: 6
Views: 2,023
Posted By thiNGS
Many thanks for your reply. I see this pattern...

Many thanks for your reply. I see this pattern with all my runs despite reagents and flow cell batches though. I wonder if my library concentration might be too high and so if I am "overloading" the...
Forum: Illumina/Solexa 01-18-2018, 08:12 AM
Replies: 6
Views: 2,023
Posted By thiNGS
Illumina NextSeq non homogenous cluster density

Hello. I am performing whole genome sequencing of bacterial strains and I got very variable cluster density (and hence signal intensity) over the four lanes of the flow cell. Has anyone ever seen...
Forum: Bioinformatics 01-30-2015, 01:51 AM
Replies: 1
Views: 1,264
Posted By thiNGS
Wink bwa settings used by MiSeq Reporter

I have performed a MiSeq 2x300 PE run using the enrichment workflow. I have performed deduplication on the FastQ files and now I want to perform alignment. I have read that if you let MiSeqReporter...
Forum: Bioinformatics 01-16-2015, 06:11 AM
Replies: 1
Views: 2,483
Posted By thiNGS
mark and remove duplicates

Hi everyone! if I mark duplicates in my BAM file using samblaster can I remove them using samtools rmdup?
I was wondering if samtools consider the duplicates flagged by the other tool and just...
Forum: Bioinformatics 01-14-2015, 05:13 AM
Replies: 0
Views: 848
Posted By thiNGS
coverage over genes using GenomeAnalysis TK

Hi. Is there a way to calculate coverage over genes getting an output where you actually can read your gene ID? I am using DepthOfCoverage with GATK but I always end up with coverage over every...
Forum: Bioinformatics 01-12-2015, 06:59 AM
Replies: 1
Views: 1,191
Posted By thiNGS
remove duplicate reads 100% sequence identity and genomic coordinates

Hi everyone. I have to analyze some paired end reads coming from a Illumina MiSeq experiment. What I want to do is removing duplicate reads that not only have the same start-end coordinates but also...
Forum: Illumina/Solexa 10-09-2014, 08:21 AM
Replies: 0
Views: 1,477
Posted By thiNGS
manifest for MiSeq

Does anyone perform library prep for MiSeq using NimbleGen SecCap EZ protocol (enrichment)? How do you prepare you manifest file since you don't use Illumina index to multiplex your samples? I am a...
Forum: Sample Prep / Library Generation 10-07-2014, 09:55 AM
Replies: 7
Views: 1,902
Posted By thiNGS
The size of the target region is 194kb. I do...

The size of the target region is 194kb.
I do perform with-bead-protocol
Forum: Sample Prep / Library Generation 10-03-2014, 02:13 PM
Replies: 7
Views: 1,902
Posted By thiNGS
The precap yield was 1.8 micrograms and i used 1...

The precap yield was 1.8 micrograms and i used 1 microgram for hybridization as recommended. The reaction is performed at 47 degrees with lid at 57 degrees. The volume of the reaction was 14.5 after...
Forum: Sample Prep / Library Generation 10-01-2014, 09:08 AM
Replies: 7
Views: 1,902
Posted By thiNGS
poor postcap yield-Kapa lib prep

Hello everyone! I am performing library generation of samples to be sequenced on Illumina HiSeq. I use kapa lib prep protocol and NimbleGen SeqCap EZ protocol to capture my target. Unfortunately, I...
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