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Forum: De novo discovery 04-26-2013, 05:51 AM
Replies: 2
Views: 2,058
Posted By AnotherHTS
Hi Liyiyuian, It looks as though you are...

Hi Liyiyuian,

It looks as though you are giving a .fasta file rather than a configuration file in the "-s" argument.
Forum: De novo discovery 04-12-2013, 08:13 AM
Replies: 4
Views: 2,339
Posted By AnotherHTS
Was the library prepared with Nextera DNA Sample...

Was the library prepared with Nextera DNA Sample Prep? If so similar bias's have been reported

http://seqanswers.com/forums/archive/index.php/t-20561.html
Forum: Academic/Non-Profit Jobs 02-15-2013, 02:26 AM
Replies: 0
Views: 1,222
Posted By AnotherHTS
Bioinformatician

A position has just become available at the MRC clinical sciences centre London:

Bioinformatician (http://www.topcareer.jobs/Vacancy/irc84330_2806.aspx)

Closing Date: 22 March 2013
Forum: Illumina/Solexa 12-20-2012, 09:19 AM
Replies: 1
Views: 1,129
Posted By AnotherHTS
Hi rohitngs, BAM/SAM is an aligned format,...

Hi rohitngs,

BAM/SAM is an aligned format, containing information about your reads and how they map against a given reference.

If you don't have alignment information it is still possible to...
Forum: RNA Sequencing 12-10-2012, 08:55 AM
Replies: 4
Views: 1,756
Posted By AnotherHTS
I am not sure if there is minimum value on...

I am not sure if there is minimum value on --segment-length.

If you still have problems perhaps you can get around it by disabling the coverage search feature with "--no-coverage-search".
Forum: Illumina/Solexa 12-10-2012, 08:51 AM
Replies: 4
Views: 1,742
Posted By AnotherHTS
I believe cluster recognition happens just once,...

I believe cluster recognition happens just once, at the beginning of the first read.
Forum: RNA Sequencing 12-07-2012, 02:15 AM
Replies: 4
Views: 1,756
Posted By AnotherHTS
have you tried decreasing the --segment-length ? ...

have you tried decreasing the --segment-length ?

Tophat splits your reads up into smaller segments (25bp by default), which it tries to align individually. If your reads are short, you may need to...
Forum: Academic/Non-Profit Jobs 03-24-2011, 04:16 AM
Replies: 0
Views: 1,770
Posted By AnotherHTS
Bioinformatician - MRC Clinical Sciences Centre

Bioinformatician
Genomics Laboratory
MRC Clinical Sciences Centre

MRC Band 5 Salary 24,176 - 27,158 pa inclusive
London W12

The CSC Genomics Laboratory...
Forum: Illumina/Solexa 01-25-2011, 02:29 AM
Replies: 4
Views: 4,752
Posted By AnotherHTS
The last column in the qseq file indicates if the...

The last column in the qseq file indicates if the read passed the signal purity filter. 1 = yes, 0 = no.

In order to pass filtering the second lowest chastity score in the first 25 cycles of a...
Forum: Bioinformatics 09-28-2010, 09:03 AM
Replies: 2
Views: 3,155
Posted By AnotherHTS
Eland - GRCh37/hg19 assembly

Hi All,

I have recently experienced a problem using the human GRCh37/hg19 assembly (from UCSC) with CASAVA/Eland.

After aligning samples with an expected random coverage to the UCSC GRCh37/hg19...
Forum: Illumina/Solexa 09-01-2010, 02:07 AM
Replies: 3
Views: 1,577
Posted By AnotherHTS
Hi josdegraaf, The gradient effect with...

Hi josdegraaf,

The gradient effect with darkened edges is something that we have observed to varying degrees on all of our Hi-Seq runs.

I believe this has been mentioned previously in the...
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