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Search: Posts Made By: aleferna
Forum: Bioinformatics 08-23-2010, 07:28 AM
Replies: 33
Views: 16,870
Posted By aleferna
@rob you mean like 200bp 0% error? where...

@rob

you mean like 200bp 0% error? where Z100 is 97.29% and default is 97.30%??
Forum: Bioinformatics 08-20-2010, 01:27 AM
Replies: 33
Views: 16,870
Posted By aleferna
@Adamo Here is the script that I've been...

@Adamo

Here is the script that I've been using. DISCLAIMER: I made this for my own data and it has not been tested on regular sequence data, so please read the code make sure you understand what...
Forum: Bioinformatics 08-18-2010, 08:52 AM
Replies: 33
Views: 16,870
Posted By aleferna
@Heng Li Well I don't care too much about...

@Heng Li

Well I don't care too much about SNPs, actually what I work with resembles more chip-seq technology. All I need to know is the position, not the alignment. I like BWA because I need to...
Forum: Bioinformatics 08-18-2010, 08:46 AM
Replies: 33
Views: 16,870
Posted By aleferna
@Adamo Sorry if I'm spamming you, I don't...

@Adamo

Sorry if I'm spamming you, I don't understand how the private messages work here. Send me a message to afer at kth.se I can send you the script to joing the 2 BWA files if you still want...
Forum: Bioinformatics 08-18-2010, 07:21 AM
Replies: 33
Views: 16,870
Posted By aleferna
Here's the behavior of a simple Blat MapQ value

Here's the behavior of a simple Blat MapQ value
Forum: Bioinformatics 08-18-2010, 07:13 AM
Replies: 33
Views: 16,870
Posted By aleferna
also if I can venture a suggestion, when I...

also if I can venture a suggestion, when I implemented the blat mapq value using S1 - S2, I noticed a big effect on the MinMapQ the MapQ threshold needed to achieve 99% specificity, as you have...
Forum: Bioinformatics 08-18-2010, 07:12 AM
Replies: 33
Views: 16,870
Posted By aleferna
Nop, I calculate score as matches - mismatches -...

Nop, I calculate score as matches - mismatches - gapbases
Forum: Bioinformatics 08-18-2010, 06:56 AM
Replies: 33
Views: 16,870
Posted By aleferna
No, I implemented a MapQ score: BestScore -...

No, I implemented a MapQ score: BestScore - 2ndBestScore (I don't divide by total score like you, this seems to improve the accuracy). I then optimized the minimum mapq score (you use a fixed one of...
Forum: Bioinformatics 08-18-2010, 06:04 AM
Replies: 33
Views: 16,870
Posted By aleferna
@lh3 No I didn't simulate indels in my...

@lh3

No I didn't simulate indels in my study, that might be the difference, but also the % of deletions and insertions vs mutations that I used simulate the characteristics of my own dataset. This...
Forum: Bioinformatics 08-17-2010, 09:45 PM
Replies: 33
Views: 16,870
Posted By aleferna
The first time I ran BWA with the long aligner I...

The first time I ran BWA with the long aligner I didn't realize that there was a short/long option and since I have both in my library I was very disappointed of BWA. I started testing algorithm...
Forum: Bioinformatics 08-17-2010, 12:33 PM
Replies: 33
Views: 16,870
Posted By aleferna
I've tested a few algorithms and the best one so...

I've tested a few algorithms and the best one so far for big 454 reads has been bwa bwasw ( the long read aligner ). I would suggest though to use z = 10 or 100 if you have a big enough computer....
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