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Forum: Bioinformatics 11-21-2014, 08:12 AM
Replies: 6
Views: 4,716
Posted By Baseless
If everything else fails, you could grab an...

If everything else fails, you could grab an Oracle VirtualBox, install a userfriendly linux flavour, face your fears and use samtools.

I do not consider myself a penguin lover, but when it comes...
Forum: Bioinformatics 10-17-2014, 06:36 AM
Replies: 7
Views: 9,131
Posted By Baseless
On GATK it is possible on many tools to use the...

On GATK it is possible on many tools to use the -nt or -nct options für using multiple threads. However, my advice is to go through every step with a benchmarking dataset to find where you get the...
Forum: Sample Prep / Library Generation 10-15-2014, 12:06 PM
Replies: 3
Views: 2,232
Posted By Baseless
And one more thing to consider on the final...

And one more thing to consider on the final product: the 16s amplicons are a diverse thing, so they are allowed to differ a bit in size.
I would not tolerate this from a PCR amplicon for...
Forum: Genomic Resequencing 10-10-2014, 06:19 AM
Replies: 4
Views: 2,709
Posted By Baseless
Like Richard, I'd first go for COSMIC, grab their...

Like Richard, I'd first go for COSMIC, grab their gene list and look who is in there. Then filter for GMAF >15% in general population and head for potential meaninful stuff (start/stop codons,...
Forum: Sample Prep / Library Generation 10-10-2014, 06:10 AM
Replies: 3
Views: 2,232
Posted By Baseless
When sampling DNA from stool I'd expect a stromg...

When sampling DNA from stool I'd expect a stromg degree of degradation and thus a high spread of sizes on gel/bioanalyzer. Even if you have DNA from blood and purify, you would rather see a smear in...
Forum: Illumina/Solexa 10-09-2014, 07:24 AM
Replies: 3
Views: 1,608
Posted By Baseless
A ok run is when its within manufacturer specs...

A ok run is when its within manufacturer specs both output and base quality wise. A good run is slightly better. And an excellent run is when no one complains about data afterwards. :)
Our best so...
Forum: Sample Prep / Library Generation 09-26-2014, 07:36 AM
Replies: 8
Views: 7,304
Posted By Baseless
@WhiteSeal: Back in my early FLX days, I had some...

@WhiteSeal: Back in my early FLX days, I had some complete losses of libraries while removing the pellet from the magnet for washing. It might be a bit of voodoo, but since I avoid disturbing the...
Forum: Bioinformatics 09-26-2014, 07:14 AM
Replies: 5
Views: 1,663
Posted By Baseless
Dear Carol, I can confirm BWA, samtools, picard...

Dear Carol,
I can confirm BWA, samtools, picard and GATK running smoothly. BCL2fastq is a bit painful, but there is an entry somewhere around this forum which has a solution using perlbrew, which...
Forum: Sample Prep / Library Generation 09-12-2014, 06:57 AM
Replies: 3
Views: 2,891
Posted By Baseless
This is like writing an email and forgetting to...

This is like writing an email and forgetting to actually put the attachment in place...sorry for the unconvenience, I edited the first response.
Forum: Sample Prep / Library Generation 09-12-2014, 06:34 AM
Replies: 8
Views: 7,304
Posted By Baseless
We have good experience drying them in a PCR...

We have good experience drying them in a PCR cycler at 37°C till a visible crack in the pellet can be seen. Usually like 3-5 mins instead of 15.
Forum: Sample Prep / Library Generation 09-12-2014, 06:07 AM
Replies: 3
Views: 2,891
Posted By Baseless
Maybe this document from ILMN helps (page 23, the...

Maybe this document from ILMN helps (page 23, the index part)?

http://supportres.illumina.com/documents/documentation/chemistry_documentation/16s/16s-metagenomic-library-prep-guide-15044223-b.pdf
Forum: Bioinformatics 08-15-2014, 08:21 AM
Replies: 3
Views: 1,364
Posted By Baseless
As above, you could use a known dataset. You...

As above, you could use a known dataset. You could also sit down and consider what happens in which step and do some checks with samtools view from your alignment. You could just grep certain...
Forum: Illumina/Solexa 04-08-2014, 08:11 AM
Replies: 15
Views: 14,199
Posted By Baseless
By the way, there actually is a barcode in the...

By the way, there actually is a barcode in the ILMN fastq, but its in the header line (note the GCNACT in the read), NOT in the sequence, unless something is special or wrong with the library:
...
Forum: Bioinformatics 04-08-2014, 08:00 AM
Replies: 4
Views: 3,571
Posted By Baseless
This will not directly solve your problem, but...

This will not directly solve your problem, but save you some time: You can run coverageBed directly from the bam file and save the time/IO needed to produce a bed file of the sequencing data first....
Forum: Illumina/Solexa 03-11-2014, 07:19 AM
Replies: 8
Views: 4,968
Posted By Baseless
PCs were upgraded, I think some memory, but they...

PCs were upgraded, I think some memory, but they got a more performant disk array for sure.

They say the cameras are too slow. But I am greatly confused that they do not offer to upgrade the...
Forum: Illumina/Solexa 02-20-2014, 06:31 AM
Replies: 8
Views: 4,968
Posted By Baseless
And the very best of it is that not all HiSeqs...

And the very best of it is that not all HiSeqs are updatable. They just told me our camera is too slow and they will not upgrade cameras.
Together with the fact they seem to plan to weed out the...
Forum: Bioinformatics 09-13-2013, 05:48 AM
Replies: 7
Views: 3,141
Posted By Baseless
Dear sBeier, It was not my intention to...

Dear sBeier,
It was not my intention to disrespect any laboratory animal. Therefore I changed the thread title.
Forum: Bioinformatics 09-13-2013, 04:56 AM
Replies: 7
Views: 3,141
Posted By Baseless
How to remove mouse reads from a human sample?

Dear forum,

I have to deal with a xenograft experiment, where a human tumor was bred in a mouse system. I have performed exome sequencing (Agilent capture, 2x100bp Illumina Sequencing), ran most...
Forum: Bioinformatics 07-18-2013, 07:11 AM
Replies: 1
Views: 1,338
Posted By Baseless
You could use fastqc for a quick evaluation of...

You could use fastqc for a quick evaluation of read quality, duplication levels and GC content.
coverageBed from the Bedtools suite and a track file of your target regions is your friend regarding...
Forum: Bioinformatics 06-14-2012, 05:23 AM
Replies: 8
Views: 2,797
Posted By Baseless
Sini, if you dont want to pay in money, look...

Sini,

if you dont want to pay in money, look at this thread:
http://seqanswers.com/forums/showthread.php?t=14038

I went through what Ulz_Peter summarizes there on my own last year and I whish...
Forum: Bioinformatics 06-14-2012, 04:26 AM
Replies: 9
Views: 5,422
Posted By Baseless
@shyam_la I reformatted mine to something...

@shyam_la

I reformatted mine to something that ensembl variant effect predictor can read and went for that during testing.

And to the others - if someone has advice which of the tools out...
Forum: Bioinformatics 06-14-2012, 04:11 AM
Replies: 8
Views: 2,797
Posted By Baseless
With just 400 candidates to go, you could also...

With just 400 candidates to go, you could also use the ENSEMBL variant effect predictor.

Maybe it is possible to contact the person who did the SNP-calling for the VCFs? Or head over to the GATK...
Forum: Illumina/Solexa 06-24-2011, 04:32 AM
Replies: 3
Views: 2,769
Posted By Baseless
Also for the HiSeq Illumina officially includes...

Also for the HiSeq Illumina officially includes enough reagents to do the indexing reads. So thats your window if you want to push it.

However, if you push it too much and have issues during...
Forum: Illumina/Solexa 05-27-2011, 02:16 AM
Replies: 3
Views: 3,577
Posted By Baseless
We had serverall issuses of cloggage since we got...

We had serverall issuses of cloggage since we got our HiSeq.
Ask your FSE for a adapter to de-clog yourself, which works by opening the front panel, connecting the correct lanes tubing to a syringe...
Forum: Sample Prep / Library Generation 08-13-2010, 11:56 AM
Replies: 41
Views: 27,773
Posted By Baseless
Bioanalyzer for sizing, pico green for...

Bioanalyzer for sizing, pico green for quantitation. We will test the qPCR once that kit arrives. I really would not miss titration if pPCR is reproducible and hits the right numbers...
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