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Forum: Bioinformatics 11-22-2013, 03:07 AM
Replies: 4
Views: 2,554
Posted By airtime
Hi, did you try bwa step "sampe" without the...

Hi,

did you try bwa step "sampe" without the "-A"?
Here is a nice discussion: http://seqanswers.com/forums/showthread.php?t=11652
if you should use it or not.

best regards,
Air
Forum: Sample Prep / Library Generation 10-26-2012, 04:39 AM
Replies: 5
Views: 2,423
Posted By airtime
Hi, what you mentioned that 95% of bases are...

Hi,

what you mentioned that 95% of bases are called means the uniformity.
But the issue is that we mapped >90% of 100 000 000 reads to the genome and then we calculate the 30% on target amount...
Forum: Sample Prep / Library Generation 10-12-2012, 01:45 AM
Replies: 5
Views: 2,423
Posted By airtime
Hi, we used this desing file...

Hi,

we used this desing file "SeqCap_EZ_Exome_v3_capture.bed" it include +- 100bp.
how deep means how many reads we get out or how many mapped?
Forum: Sample Prep / Library Generation 10-11-2012, 11:28 PM
Replies: 5
Views: 2,423
Posted By airtime
Hi, there are design files (.bed) with...

Hi,

there are design files (.bed) with region information. And that reads mapped to the genome, including a region from the design file too, are on target.
Forum: Sample Prep / Library Generation 09-27-2012, 12:55 AM
Replies: 5
Views: 2,423
Posted By airtime
Exome Sequencing with nimblegen SeqCap EZ v3

Hi,

we working with a GAllx from Illumina and have good experience with nimblegen SeqCap EZ v2 (on target).
We compare the nimblegen SeqCap EZ v3 and Illumina TrueSeq exome kits and the results...
Forum: Bioinformatics 05-09-2012, 01:31 AM
Replies: 5
Views: 5,242
Posted By airtime
Hi, ok. How big are your files and your RAM?...

Hi,

ok. How big are your files and your RAM? If you convert sam to uncompressed bam is their size similar?

regards Air
Forum: Bioinformatics 05-08-2012, 07:16 AM
Replies: 5
Views: 5,242
Posted By airtime
Hi, did you sort your bam file before? ...

Hi,

did you sort your bam file before?
Some further proceeding steps would be helpful (like full command execution).
Forum: Bioinformatics 03-23-2012, 12:06 AM
Replies: 16
Views: 12,792
Posted By airtime
Hi, I found it here: ...

Hi,

I found it here:
http://www.massgenomics.org/2012/03/5-things-to-know-about-samtools-mpileup.html

It depends on samtool parameters, this could be the reason that Kobold didn't find out.
...
Forum: Bioinformatics 03-21-2012, 03:12 AM
Replies: 16
Views: 12,792
Posted By airtime
Hi, Ifound this info at VarScan 2...

Hi,

Ifound this info at VarScan 2 description:

Base alignment quality (BAQ) computation is turned on by default. BAQ is a phred-like score representing the probability that a read base is...
Forum: Bioinformatics 03-20-2012, 07:21 AM
Replies: 16
Views: 12,792
Posted By airtime
Hi, VarScan2 is published try it out and...

Hi,

VarScan2 is published try it out and share your experience.
It should be better than the first version (mentioned in the paper) and also outperformce the SomaticSniper.
Forum: Bioinformatics 03-20-2012, 07:10 AM
Replies: 2
Views: 955
Posted By airtime
Hi Phil, if you have *.bed files for the...

Hi Phil,

if you have *.bed files for the corresponding regions, than you can use BEDTools for count reads and many other things.

Air
Forum: Bioinformatics 03-09-2012, 04:37 AM
Replies: 0
Views: 1,553
Posted By airtime
base calling bustard or external tools?

Hi,

we are working with a GaXll Sequencer from Illumina and screening for SNP's. I read some publications about external Basecaller and thought about their useability.

There are many external...
Forum: Bioinformatics 11-29-2011, 01:04 AM
Replies: 6
Views: 3,005
Posted By airtime
Hi fongchun, did you know which version your...

Hi fongchun,

did you know which version your SCS at the Sequence-PC is?
Or how get you the qseq files?
I suppose that old versions through qseq files (and so it must be phred + 64), the new...
Forum: Bioinformatics 10-17-2011, 01:21 AM
Replies: 1
Views: 2,033
Posted By airtime
functional prediction SNP

Hi,

I have a list of SNP resulting from exome Re-Sequencing of tumor/normal human samples and GATK analyses. Now I searching Softwaretools for prediction (or better :)) which analyse Mutation...
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