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Forum: Illumina/Solexa 02-03-2015, 06:07 PM
Replies: 53
Views: 70,656
Posted By frozenlyse
Which means that people will be doing more runs...

Which means that people will be doing more runs per year which means a lot more reagent sales for Illumina!
Forum: Bioinformatics 01-13-2015, 02:58 PM
Replies: 136
Views: 40,566
Posted By frozenlyse
Hi Felix - I'm writing the methods sections for a...

Hi Felix - I'm writing the methods sections for a few WGBS papers where I've used trim_galore, is there a paper I can cite for it?
Forum: Epigenetics 01-07-2015, 10:55 PM
Replies: 3
Views: 1,654
Posted By frozenlyse
The first row is read 1, and the second row is...

The first row is read 1, and the second row is read 2 - you can tell from the SAM flag (second column)

99 == 0x01 + 0x02 + 0x20 + 0x40 which translates to "template having multiple segments in...
Forum: Oxford Nanopore 10-01-2014, 07:14 PM
Replies: 47
Views: 17,189
Posted By frozenlyse
hah yeah don't mind me, mind was off on a tangent...

hah yeah don't mind me, mind was off on a tangent and haven't had coffee yet!
Forum: Oxford Nanopore 10-01-2014, 07:00 PM
Replies: 47
Views: 17,189
Posted By frozenlyse
Also a naive 4^5 state model would throw out the...

Also a naive 4^5 state model would throw out the redundant information of each 5-mer signal overlapping the previous basecalls
Forum: Epigenetics 09-25-2014, 06:44 PM
Replies: 2
Views: 1,210
Posted By frozenlyse
Isn't there already an amplification step after...

Isn't there already an amplification step after the enrichment (with primers against the Illumina adaptors which were ligated prior to the enrichment)?
Forum: Bioinformatics 09-01-2014, 03:58 AM
Replies: 649
Views: 168,236
Posted By frozenlyse
kevinrun - what does fastqc look like on your...

kevinrun - what does fastqc look like on your forward and reverse reads?

We've recently switched over to the same kit, and now only do 71bp PE reads (we can get that out of 2 50 cycle SBS kits). I...
Forum: Ion Torrent 08-18-2014, 11:09 PM
Replies: 6
Views: 4,173
Posted By frozenlyse
I wouldnt use bismark on ion torrent data as it...

I wouldnt use bismark on ion torrent data as it is going to have a lot of indels due to homopolymers, and bismark doesnt run bowtie2 in local alignment mode - I would try...
Forum: Bioinformatics 06-03-2014, 04:48 PM
Replies: 366
Views: 179,900
Posted By frozenlyse
Hi Simon, Thanks for all your work on the...

Hi Simon,
Thanks for all your work on the update! One feature which would be really nice is the ability to run fastqc on paired end data and to show the reports for each read next to each other in...
Forum: Bioinformatics 03-12-2014, 05:34 PM
Replies: 649
Views: 168,236
Posted By frozenlyse
This may become moot as bowtie2 can now support...

This may become moot as bowtie2 can now support large genomes so separate alignments for different strands of the genome could be a thing of the past and simplify bisulfite alignment quite a bit! Of...
Forum: Bioinformatics 03-05-2014, 09:27 PM
Replies: 8
Views: 3,308
Posted By frozenlyse
convert your sam to bam and then index using...

convert your sam to bam and then index using samtools, load into IGV
Forum: Bioinformatics 03-04-2014, 04:26 PM
Replies: 8
Views: 3,308
Posted By frozenlyse
That just looks like custom data loaded to UCSC?

That just looks like custom data loaded to UCSC?
Forum: Bioinformatics 02-17-2014, 03:59 PM
Replies: 62
Views: 25,323
Posted By frozenlyse
That's not a good way to get people to use your...

That's not a good way to get people to use your software! :confused::confused:
Forum: Epigenetics 02-10-2014, 04:45 PM
Replies: 1
Views: 3,374
Posted By frozenlyse
Strange bisulfite libraries

Our lab is doing more and more WGBS libraries (human) - and we sporadically sequence a weird library that aligns poorly (~15% vs usual ~80% with bismark2) and has a weird base composition profile -...
Forum: Bioinformatics 11-21-2013, 02:20 PM
Replies: 13
Views: 5,565
Posted By frozenlyse
Also the HP has ECC ram which is a helluva lot...

Also the HP has ECC ram which is a helluva lot more expensive per GB (but looks expandable up to 128Gb which may be useful down the track!)
Forum: Epigenetics 11-20-2013, 06:39 PM
Replies: 15
Views: 8,441
Posted By frozenlyse
I'm not familiar with those kits, but wouldn't...

I'm not familiar with those kits, but wouldn't you expect a much lower % of cytosines in a bisulfite library? I usually get ~1%.

Also could your size distribution graphs be plotting paired end...
Forum: Epigenetics 11-20-2013, 06:31 PM
Replies: 4
Views: 2,023
Posted By frozenlyse
Bisulfite sequencing and solid is a very very...

Bisulfite sequencing and solid is a very very very very very very very very very very very very very bad idea.
Forum: Sample Prep / Library Generation 10-09-2013, 02:45 PM
Replies: 2
Views: 2,153
Posted By frozenlyse
Truseq works on double stranded DNA - if your...

Truseq works on double stranded DNA - if your cDNA is single stranded, you will have to synthesise a second strand before doing the 'end repair' ie end blunting then a tailing.
Forum: Pacific Biosciences 10-01-2013, 05:54 PM
Replies: 3
Views: 3,005
Posted By frozenlyse
Our cluster has 512Gb ram per 64 core node, and...

Our cluster has 512Gb ram per 64 core node, and RAM has never been a problem.
Forum: Sample Prep / Library Generation 09-17-2013, 05:24 PM
Replies: 3
Views: 2,085
Posted By frozenlyse
100kb is a tricky area to target at the moment......

100kb is a tricky area to target at the moment... If you have a lot of DNA for your samples you could look into doing multiplexed sequence capture ie make barcoded libraries for each sample, pool x...
Forum: Illumina/Solexa 09-12-2013, 03:02 PM
Replies: 3
Views: 4,263
Posted By frozenlyse
I thought MiSeq basecalling could handle even...

I thought MiSeq basecalling could handle even single amplicons with the latest software updates?
Forum: Bioinformatics 09-03-2013, 04:36 AM
Replies: 649
Views: 168,236
Posted By frozenlyse
Ah sure, that makes sense - I may test it out for...

Ah sure, that makes sense - I may test it out for myself on the unaligned read from a cancer cell line with some known translocations and see if anything falls apart - if I get around to testing it...
Forum: Bioinformatics 09-03-2013, 04:19 AM
Replies: 649
Views: 168,236
Posted By frozenlyse
Hi, I was wondering about using WGBS data...

Hi,

I was wondering about using WGBS data for structural variant prediction - according to the bismark manual, the bowtie2 paired end options --no-mixed and --no-discordant are always set on - is...
Forum: Bioinformatics 08-07-2013, 06:13 PM
Replies: 2
Views: 1,968
Posted By frozenlyse
In my pipeline for MiSeq amplicon analysis I...

In my pipeline for MiSeq amplicon analysis I align the reads keeping the primers on, and then just ignore the primer areas in downstream analysis.
Forum: Bioinformatics 07-25-2013, 05:59 PM
Replies: 649
Views: 168,236
Posted By frozenlyse
What kind of weird results did you get? I've...

What kind of weird results did you get? I've always used it on position sorted bam files (had no idea it wanted name sorting), and WGBS data I've got correlates really well with HM450 arrays...
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