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Forum: Illumina/Solexa 12-12-2011, 08:05 AM
Replies: 6
Views: 4,713
Posted By dvh
thanks for your graph peromhc. it does look...

thanks for your graph peromhc.

it does look like we might be able to make use of HiSeq+Truseq v3 data out to 125-130bp as pmiguel suggests.

for the application we want (amplicon sequencing with...
Forum: Illumina/Solexa 12-06-2011, 09:35 AM
Replies: 6
Views: 4,713
Posted By dvh
>100bp hiseq read length ?

Hi,

Has anyone experience of >100bp reads with HiSeq1000/2000 ?
(TruSeq v3 chemistry)

We could make good use of slightly longer reads than 100bp.
We are also going to waste reagents from a...
Forum: Bioinformatics 04-01-2010, 01:05 PM
Replies: 4
Views: 4,790
Posted By dvh
thanks sm, in fact we are already using seattle...

thanks sm, in fact we are already using seattle seq annotation for SNPs, and it is great.
Doesnt do small indels though - at least not on the public site...?
dvh
Forum: Bioinformatics 03-31-2010, 01:54 PM
Replies: 4
Views: 4,790
Posted By dvh
exome indel annotation

Hi,

Can anybody point me to good tools for annotating small (<15bp) indels from human exome resequencing.

Effect on protein coding sequence (frameshift/stop, in frame), known in dbSNP, etc.
...
Forum: Illumina/Solexa 02-04-2010, 04:40 AM
Replies: 2
Views: 9,890
Posted By dvh
GA pipeline chastity/purity filters

Anyone have experience of changing the default settings of the filtering parameters in the GA pipeline used to remove low quality reads?

From the manual "The default filter is equivalent to:...
Forum: Illumina/Solexa 10-07-2009, 05:35 AM
Replies: 7
Views: 4,184
Posted By dvh
Thats just a sampling issue. Say there are...

Thats just a sampling issue.

Say there are only 1000 unique molecules in the library:

If you topo/sanger sequence x100, only a few will look like duplicates.

But if you nex-gen sequence...
Forum: Illumina/Solexa 07-13-2009, 06:47 AM
Replies: 1
Views: 3,364
Posted By dvh
denaturation step prior to cluster generation

Hi,

Has anybody made clusters on a GAII flowcell using different protocol to Illumina's?

We have a low conc library to sequence. Doing more PCR has lead to clonal reads (~50% of reads duplicate...
Forum: Bioinformatics 06-23-2009, 04:14 AM
Replies: 2
Views: 3,236
Posted By dvh
Never seen that in quite a few RNAseq runs. ...

Never seen that in quite a few RNAseq runs.

Someone added more cycle seq reagent at the wrong time, banged the machine, brief power cut, etc?

You could always N out this base position in all...
Forum: Bioinformatics 06-11-2009, 02:52 AM
Replies: 3
Views: 2,005
Posted By dvh
novoalign will do variable read lengths, and has...

novoalign will do variable read lengths, and has all maq functionality.
Forum: Illumina/Solexa 05-28-2009, 05:36 AM
Replies: 7
Views: 4,055
Posted By dvh
pipeline 1.4 versus 1.3

Thought this might be of interest.

Illumina say the latest version of the Pipeline (v1.4) has better image analysis (Firecrest). To test this claim, I analysed both ways a 70bpx2 PhiX lane from a...
Forum: Illumina/Solexa 03-19-2009, 11:13 AM
Replies: 3
Views: 2,886
Posted By dvh
I had a look in our data, we dont seem to see...

I had a look in our data, we dont seem to see this. GAII 45bp or 70bp x2 PE. Human resequencing. Novoalign.
Forum: Bioinformatics 03-09-2009, 09:19 AM
Replies: 2
Views: 2,225
Posted By dvh
Which version of solexa/illumina Pipeline? ...

Which version of solexa/illumina Pipeline?

Base call quality score output in GERALD folder 'fastq' files seems to have changed from Pipeline 1.0 to 1.3.2.

See...
Forum: Illumina/Solexa 02-26-2009, 10:59 AM
Replies: 7
Views: 2,737
Posted By dvh
another source: the current human genome sequence...

another source: the current human genome sequence is imperfect. there are likely sequences which are in fact repeats but do not appear so in the current genome assembly.

if we see 'read-towers' we...
Forum: Illumina/Solexa 01-28-2009, 03:43 AM
Replies: 19
Views: 37,134
Posted By dvh
CASAVA, Pipeline 1.3

I've just looked through the just released CASAVA manual. Whilst it would seem to have some new tools for visualising/calling SNPs and RNAseq, it seems totally dependent on ELAND alignments.

We...
Forum: Bioinformatics 01-14-2009, 02:35 PM
Replies: 99
Views: 35,943
Posted By dvh
As well as the paired-end read Q above, does...

As well as the paired-end read Q above, does mapview cope with gapped alignments in each read? (e.g. where maqview, developed alongside maq package, does not).
I would also be interested to hear...
Forum: Illumina/Solexa 01-06-2009, 11:49 AM
Replies: 145
Views: 300,979
Posted By dvh
novoalign has 5' and 3' removal of adapter...

novoalign has 5' and 3' removal of adapter sequences prior to alignment. works well.
david
Forum: Bioinformatics 12-18-2008, 03:43 PM
Replies: 16
Views: 5,008
Posted By dvh
Nav, Am interested: 1. sweet spot=5...

Nav,

Am interested:

1. sweet spot=5 errors, but in what read length - 36bp, 45bp, 70bp etc ?

2. Did you remove homopolymer, and "low base quality across entire read" reads first, or rely on...
Forum: Bioinformatics 12-18-2008, 09:00 AM
Replies: 16
Views: 5,008
Posted By dvh
We've not been able to persuade GA Pipeline 1.0...

We've not been able to persuade GA Pipeline 1.0 to give decent calibrated base call quality score results for our 45bp reads. Is I think due to use of ELAND and that eland_extended isnt great for...
Forum: Bioinformatics 12-16-2008, 11:43 AM
Replies: 23
Views: 7,178
Posted By dvh
Sure, but it is a fiddle to split the reads,...

Sure, but it is a fiddle to split the reads, rejoin etc esp with multiple lanes and flowcells to analyse. There are also some new features just in the multithreaded version and enhanced support....
Forum: Bioinformatics 12-16-2008, 11:24 AM
Replies: 23
Views: 7,178
Posted By dvh
novoalign

I'd highly recommend novoalign as well. Use of quality scores, gapped alignments for indels, etc.

Even though an academic institution, we bought the multithreaded version. Runs ~16X faster on our...
Forum: Bioinformatics 12-12-2008, 03:17 PM
Replies: 6
Views: 2,342
Posted By dvh
Note also the issue with maqview and incorrect...

Note also the issue with maqview and incorrect display of reads with small indels, and Heng Li's response re samtools - see the maq help list.
david
Forum: Bioinformatics 12-01-2008, 03:48 PM
Replies: 4
Views: 4,096
Posted By dvh
Try just: ANALYSIS sequence_pair ...

Try just:
ANALYSIS sequence_pair
SEQUENCE_FORMAT --fastq
nothing else.
Forum: RNA Sequencing 11-19-2008, 10:55 PM
Replies: 9
Views: 11,310
Posted By dvh
Yes. We've done paired end RNAseq - partly...

Yes. We've done paired end RNAseq - partly because of mixed sample type (some DNAseq etc) flow cells.

The paired end info is useful for novel gene expression and splice junction discovery.

For...
Forum: Bioinformatics 11-18-2008, 01:58 PM
Replies: 7
Views: 4,584
Posted By dvh
Note there are some default filters on maq pileup...

Note there are some default filters on maq pileup output:
-m INT Maximum number of mismatches allowed for a read to be used [7]
-Q INT Maximum allowed number of quality values of mismatches [60]...
Forum: Illumina/Solexa 11-10-2008, 03:46 PM
Replies: 3
Views: 1,816
Posted By dvh
There are some proprietary modifications to...

There are some proprietary modifications to Illumina's oligos.
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