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Search took 0.00 seconds. Search: Posts Made By: vl80
Forum: Illumina/Solexa 09-13-2014, 01:28 AM
Replies: 0
Views: 1,065
Posted By vl80
sequencing 1000 amplicons on miseq

Hi,

We are developing an amplicom sequencing project where the consensus primers for enrichment can be designed with amplicons between 800 to 1100 bp only. However, there is another catch, we do...
Forum: Bioinformatics 07-15-2014, 11:25 PM
Replies: 1
Views: 1,272
Posted By vl80
Unable to see BAM files from CLC on geneious or IGV

We got BAM files from our service provider on CLC workbench. However, it is not possible to visualize them on both geneious and IGV for some reason. Importation fails in Geneious. I think the issue...
Forum: Sample Prep / Library Generation 06-09-2014, 12:06 AM
Replies: 1
Views: 4,488
Posted By vl80
Nextera XT vs TruSeq PCR free

I have previously used the TruSeq DNA kit (only once) and now need to move on to use either Nextera XT or TruSeq PCR free kits and perform the whole library prep alone for the first time.
I would...
Forum: Bioinformatics 05-28-2014, 03:23 PM
Replies: 4
Views: 1,218
Posted By vl80
Thanks a lot. Unfortunately, the not tech savy...

Thanks a lot. Unfortunately, the not tech savy group.
Forum: Bioinformatics 05-27-2014, 06:06 PM
Replies: 4
Views: 1,218
Posted By vl80
Free GUI based sortware for off instrument SMRT analysis

Are there any free GUI based software or cloud platform for basic analysis of small genomes (2x10^6bp) (de novo assembly, alignment, epigenetic modification ID) for Pacbio RS II based data that can...
Forum: Bioinformatics 12-03-2013, 08:20 PM
Replies: 2
Views: 1,713
Posted By vl80
Just adding to the above question, has anyone had...

Just adding to the above question, has anyone had any experiences with barcode/index (inhouse) mistmatch between R1 and R2 and the percentage of such mistmatched reads?We are really stuck with the...
Forum: Bioinformatics 12-03-2013, 04:29 PM
Replies: 2
Views: 1,713
Posted By vl80
Barcode mismatch R1 and R2

Hi,

We are demultiplexing some in house barcodes, 5 nt in length as mentioned in a previous post for 2 x 150 Miseq runs
When this is done, there is a very high frequency of mismatch between R1...
Forum: Bioinformatics 12-02-2013, 03:53 PM
Replies: 3
Views: 3,925
Posted By vl80
GenoMax, thank you, I read this earlier but more...

GenoMax, thank you, I read this earlier but more that that our problem is what Jackie has pointed out.
Forum: Bioinformatics 12-01-2013, 11:17 PM
Replies: 3
Views: 3,925
Posted By vl80
Unhappy De-multiplexing, carryover from sample with highest reads?

Hello,
I use in house indexes (5nt) to tag my amplicons and pool 10 such samples and subject the pooled "sample" to library prep on TruSeq without fragmentation.

After demultiplexing for Illumina...
Forum: Bioinformatics 04-06-2013, 05:20 PM
Replies: 0
Views: 1,128
Posted By vl80
SAM/BAM header in Galaxy

Is there a way to get the header file by default in the SAM output of alignment in Galaxy? I know that there is a header replacement option, but I just want know if this is pobbile by default.
Even...
Forum: Bioinformatics 04-05-2013, 04:46 AM
Replies: 9
Views: 2,455
Posted By vl80
Yes I did, unfortunately no reply yet. I tried to...

Yes I did, unfortunately no reply yet. I tried to send an error message too. Still no feed back.
Forum: Bioinformatics 04-04-2013, 02:32 PM
Replies: 9
Views: 2,455
Posted By vl80
I am using the Galaxy site at...

I am using the Galaxy site at https://main.g2.bx.psu.edu/ Not a locally downloaded version..
Forum: Bioinformatics 04-04-2013, 09:17 AM
Replies: 9
Views: 2,455
Posted By vl80
This is the error I get on trying to get the...

This is the error I get on trying to get the coverage stats...

An error occurred with this dataset: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main [Thu Apr 04 12:10:28 EDT 2013]...
Forum: Bioinformatics 04-04-2013, 06:37 AM
Replies: 9
Views: 2,455
Posted By vl80
Actually, alignment went OK, my mistake in...

Actually, alignment went OK, my mistake in posting.
When I wanted to convert SAM-BAM an error came. Also, I tried to filter the alined SAM data, the number of sequences remaining in the end were...
Forum: Bioinformatics 04-04-2013, 06:15 AM
Replies: 9
Views: 2,455
Posted By vl80
My ref sequences are in FASTA formates with...

My ref sequences are in FASTA formates with compatible lengths per line
However the file is something like

>Ref_amplicon1
AAAACCGGTTTAA
>Ref_amplicon2
GGTTCCAAAAAA
>Ref_Amplicon3
CCCTTGGAAA
Forum: Bioinformatics 04-04-2013, 05:38 AM
Replies: 9
Views: 2,455
Posted By vl80
Bowtie on Galaxy - multiple amplicon sequences instead of reference genome

I am trying to use Bowtie in Galaxy via the web GUI to align Miseq generated amplicons. Our amplicons are from a multiplex PCR and thus instead of a single reference sequence we have a number of (27 ...
Forum: Bioinformatics 04-01-2013, 06:14 PM
Replies: 0
Views: 1,015
Posted By vl80
Consensus sequence/ positional nucleotide summary in IGV

Is it possible to obtain a positional nucleotide summary and a consensus sequence using IGV? I am using IGV to visualise an alignment done usine Miseq reporter. My aim is not to identify mutations,...
Forum: Bioinformatics 03-25-2013, 06:44 AM
Replies: 0
Views: 1,382
Posted By vl80
Basic Bioinformatics Courses

Hi,
Does anyone know of introductory - intermediate level bioinformatics short courses conducted preferably in Asia which may be particularly targetting pathogen genomics? Mostly interested in NGS...
Forum: Illumina/Solexa 03-21-2013, 04:57 PM
Replies: 3
Views: 1,622
Posted By vl80
It does work! Now the next step would be to see...

It does work! Now the next step would be to see if an annotation file can be created for the pseudo genome so that the Miseq reporter can put out the results with annotation. The annotation would be...
Forum: Illumina/Solexa 03-13-2013, 10:31 PM
Replies: 3
Views: 1,622
Posted By vl80
String of short sequences as a genome for Miseq reporter

We did some PCR sequencing on Miseq and are trying to see if we could use a stringed together sequence of all amplicons to creat a pseudogenome and input for Miseq reporter in the resequencing...
Forum: Bioinformatics 03-08-2013, 12:13 AM
Replies: 3
Views: 3,386
Posted By vl80
Thank you very much. Just a few "dummy"...

Thank you very much. Just a few "dummy" questions..
The file that we get from Miseq after decoding of the illumima index is in the format of a fastaQ file. As a clinician who is at complete loss...
Forum: Bioinformatics 03-07-2013, 06:16 PM
Replies: 3
Views: 3,386
Posted By vl80
De - multiplexing

We have incorporated unique tags/indexes/barcodes (5nt long) to our inhouse PCR primers. After PCR,amplicons from 8 samples were cleaned and pooled together in an equimolar manner and we have 10 such...
Forum: Sample Prep / Library Generation 02-15-2013, 04:14 AM
Replies: 1
Views: 2,437
Posted By vl80
PCR product quantification

We plan to use uniq adaptor tagged primers for a PCR and then pool PCR products of about 5 samples together for one TruSeq index and follow the TruSeq protocol skipping fragmentation.
Pooling...
Forum: Illumina/Solexa 02-14-2013, 03:25 PM
Replies: 6
Views: 2,622
Posted By vl80
Thank you very much for both suggestions. Would...

Thank you very much for both suggestions. Would do so.
Forum: Illumina/Solexa 02-14-2013, 01:03 PM
Replies: 6
Views: 2,622
Posted By vl80
Thank you very much. Yes, I read that in Trueseq...

Thank you very much. Yes, I read that in Trueseq the requirement is for 1ug. The tests would be done for us for the first time at a commercial venture. Thier requirement states that the conc of DNA...
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