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Search: Posts Made By: Zaag
Forum: Bioinformatics 03-11-2016, 07:51 AM
Replies: 6
Views: 838
Posted By Zaag
True, but you can leave the adapters on and just...

True, but you can leave the adapters on and just cut adapter + 4 bp

I know PrinSeq has this option:
-trim_right

Trim sequence at the 3'-end by trim_right positions...
Forum: Bioinformatics 03-11-2016, 07:35 AM
Replies: 6
Views: 838
Posted By Zaag
CROP: Cut the read to a specified length

CROP: Cut the read to a specified length
Forum: Sample Prep / Library Generation 10-19-2015, 04:07 AM
Replies: 65
Views: 36,987
Posted By Zaag
I have sent some of them out this morning, I...

I have sent some of them out this morning, I don't know when I get my results, but I will post the bio-analyser traces and some sequencing QC when I get it back.
Forum: Bioinformatics 08-22-2015, 04:31 AM
Replies: 7
Views: 976
Posted By Zaag
Sorry if you already understood but you need to...

Sorry if you already understood but you need to install contra again with python2.7 for it to work.
Forum: Bioinformatics 08-21-2015, 06:56 AM
Replies: 7
Views: 976
Posted By Zaag
Did you reinstall before trying with python2.7?

Did you reinstall before trying with python2.7?
Forum: Ion Torrent 08-12-2015, 07:52 AM
Replies: 28
Views: 43,242
Posted By Zaag
And is it already delivering on the read lengths...

And is it already delivering on the read lengths and output promised for the end of 2013?
Forum: SOLiD 07-01-2015, 04:46 AM
Replies: 5
Views: 3,097
Posted By Zaag
GQ does not tell you anything about the variant...

GQ does not tell you anything about the variant quality. GQ tells you about how certain the HC is about the zygosity.

About the deletions: do they disappear if you use this option in the variant...
Forum: Sample Prep / Library Generation 06-30-2015, 06:56 AM
Replies: 65
Views: 36,987
Posted By Zaag
I used this protocol and got this after...

I used this protocol and got this after adapter-PCR:
...
Forum: Bioinformatics 04-21-2015, 05:24 AM
Replies: 8
Views: 991
Posted By Zaag
See if it occurs more often and if it is always...

See if it occurs more often and if it is always on the same strand, if so just turn them around.
Forum: Bioinformatics 02-13-2015, 04:26 AM
Replies: 3
Views: 2,681
Posted By Zaag
We also tried Mutect and it indeed calls more...

We also tried Mutect and it indeed calls more true low frequency mutations.

@spreeth84: What parameters do you tweak? Do you know if there is a proper manual?
Forum: 454 Pyrosequencing 02-10-2015, 08:49 AM
Replies: 6
Views: 2,560
Posted By Zaag
From what I understand they'll give you the...

From what I understand they'll give you the programs you need if you ask nicely:

http://seqanswers.com/forums/showpost.php?p=8278&postcount=13

I think there also are some open source variants...
Forum: Bioinformatics 02-10-2015, 08:42 AM
Replies: 12
Views: 2,816
Posted By Zaag
Not every base. BWA gives every possible...

Not every base.

BWA gives every possible aligmments a score and I can imagine that having 4 high quality mismatches at the end of the read yields a higher score then clipping of the 4 bases;
...
Forum: General 02-10-2015, 07:33 AM
Replies: 1
Views: 729
Posted By Zaag
Rule of thumb is if you can measure it you can...

Rule of thumb is if you can measure it you can sequence it.
Forum: Bioinformatics 02-10-2015, 07:21 AM
Replies: 12
Views: 2,816
Posted By Zaag
M stands for match or mismatch in the CIGAR ...

M stands for match or mismatch in the CIGAR

http://zenfractal.com/assets/images/cigar_ops.png
Forum: Bioinformatics 02-10-2015, 07:19 AM
Replies: 12
Views: 2,816
Posted By Zaag
I guess 4 mismatches at the end of the read is...

I guess 4 mismatches at the end of the read is less penalty than clipping of the 4. What are the qualities of the 4 bases?
Forum: 454 Pyrosequencing 02-10-2015, 07:17 AM
Replies: 6
Views: 2,560
Posted By Zaag
Well if that really is what you want you could go...

Well if that really is what you want you could go from sff to fasta, alter the fasta and go back to sff. You can use the sfftools/sffinfo provided by Roche.
Forum: Bioinformatics 02-04-2015, 08:32 AM
Replies: 12
Views: 2,816
Posted By Zaag
use bwa-mem

use bwa-mem
Forum: Ion Torrent 01-08-2015, 07:38 AM
Replies: 21
Views: 32,215
Posted By Zaag
You say the Amplicon PCR product, is that before...

You say the Amplicon PCR product, is that before or after digestion with the infamous "FuPa"?
Forum: Illumina/Solexa 12-18-2014, 04:49 AM
Replies: 3
Views: 1,024
Posted By Zaag
Trimmomatic can remove anything you put in a...

Trimmomatic can remove anything you put in a fasta file.
Forum: Sample Prep / Library Generation 12-18-2014, 03:28 AM
Replies: 3
Views: 1,130
Posted By Zaag
If you are building an amplicon library you will...

If you are building an amplicon library you will only have PCR duplicates, so you leave them in. If you build a shotgun library you'll want to remove them.
Forum: Illumina/Solexa 12-08-2014, 05:04 AM
Replies: 2
Views: 1,325
Posted By Zaag
It will complain, but you can switch RFID tags...

It will complain, but you can switch RFID tags between flowcells.
Forum: Illumina/Solexa 10-10-2014, 06:29 AM
Replies: 3
Views: 960
Posted By Zaag
High percentage Q30 or higher bases High amount...

High percentage Q30 or higher bases
High amount of data
High percentage reads that reach full length
Forum: Sample Prep / Library Generation 10-10-2014, 06:21 AM
Replies: 7
Views: 1,129
Posted By Zaag
How do you clean up after PCR?

How do you clean up after PCR?
Forum: Sample Prep / Library Generation 10-07-2014, 08:47 AM
Replies: 7
Views: 1,129
Posted By Zaag
What is the size of the capture? Did you...

What is the size of the capture?

Did you include the streptavidin beads in the PCR?
Forum: Bioinformatics 10-01-2014, 02:08 AM
Replies: 1
Views: 1,086
Posted By Zaag
http://statgenpro.psychiatry.hku.hk/limx/kggseq/do...

http://statgenpro.psychiatry.hku.hk/limx/kggseq/download.php
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