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Search: Posts Made By: xied75
Forum: Bioinformatics 03-21-2013, 02:58 PM
Replies: 10
Views: 5,497
Posted By xied75
But I have pure female reads that can map a lot Y?

But I have pure female reads that can map a lot Y?
Forum: Bioinformatics 03-21-2013, 11:42 AM
Replies: 1
Views: 934
Posted By xied75
Given your data is PE, there is no reason the...

Given your data is PE, there is no reason the number shouldn't match really. Could be pairing messed up. How many reads do you have in each fastq then?

Best,

Dong
Forum: Bioinformatics 03-09-2013, 02:46 PM
Replies: 11
Views: 2,823
Posted By xied75
You can send private msg or email via seqanswers...

You can send private msg or email via seqanswers in fact.
Forum: Bioinformatics 03-09-2013, 11:47 AM
Replies: 11
Views: 2,823
Posted By xied75
Ok. You can leave your file over dropbox.

Ok. You can leave your file over dropbox.
Forum: Bioinformatics 03-08-2013, 02:22 PM
Replies: 3
Views: 1,810
Posted By xied75
How big is your dataset? What if you can't hold...

How big is your dataset? What if you can't hold them in one physical machine? You'll scale-up or scale-out?
Forum: Bioinformatics 03-07-2013, 10:22 AM
Replies: 11
Views: 2,823
Posted By xied75
No no I wasn't suggesting you always do this,...

No no I wasn't suggesting you always do this, this is only to troubleshooting where the problem might be, by running directly with BWA you can figure out if this is something to do with BWA or it's...
Forum: Bioinformatics 03-07-2013, 08:52 AM
Replies: 8
Views: 2,393
Posted By xied75
I tried your data, BWA ALN with -n 10 definitely...

I tried your data, BWA ALN with -n 10 definitely changed the results. Also your reads seems in different lengths. For ALN there are so many options to play with, e.g. -l for seed length, -k for max...
Forum: Bioinformatics 03-07-2013, 06:03 AM
Replies: 8
Views: 2,393
Posted By xied75
No this means that when a reads can be mapped to...

No this means that when a reads can be mapped to many places and the mapping quality are same then one hit will be chosen randomly to output into the sam file.

If you want more hits you should...
Forum: Bioinformatics 03-05-2013, 05:33 AM
Replies: 11
Views: 2,823
Posted By xied75
How about you try to run BWA directly? See what...

How about you try to run BWA directly? See what happens.
Forum: Academic/Non-Profit Jobs 03-01-2013, 07:42 AM
Replies: 0
Views: 685
Posted By xied75
The author of BOW and Fourtytwo is looking for a job

BOW is here http://bow.codeplex.com
Fourtytwo is here http://www.fourty-two.org

This guy does everything on Windows, that's the only catch.
Immediately available,

Best,

Dong
Forum: Bioinformatics 03-01-2013, 07:19 AM
Replies: 11
Views: 2,823
Posted By xied75
-n 0 should work at least I tried that before....

-n 0 should work at least I tried that before. How long is your reads? When you don't do -n 0, did you get any good alignment, what percentage?

Best,

Dong
Forum: Bioinformatics 02-07-2013, 03:11 AM
Replies: 16
Views: 3,964
Posted By xied75
Hi, Joe, Those commands look alright. When...

Hi, Joe,

Those commands look alright. When you said

You mean when you tried to do sorting and dup remove on your newly generated bam you get those error msg or you mean after you did sorting...
Forum: Bioinformatics 02-06-2013, 08:37 AM
Replies: 16
Views: 3,964
Posted By xied75
Need to look at your command line then.

Need to look at your command line then.
Forum: Bioinformatics 02-06-2013, 08:09 AM
Replies: 16
Views: 3,964
Posted By xied75
then your bam is not correct. Try use hexdump to...

then your bam is not correct. Try use hexdump to see it.
Forum: Bioinformatics 02-05-2013, 03:03 AM
Replies: 8
Views: 3,463
Posted By xied75
Hi, Jom, Did you notice that in your command...

Hi, Jom,

Did you notice that in your command your two sai files are the same name, but it should be one sai from read 1, another sai from read2.

This should have nothing to do with the '1888]'...
Forum: Bioinformatics 02-01-2013, 03:06 AM
Replies: 4
Views: 4,262
Posted By xied75
Yes because sampe is single thread no matter how...

Yes because sampe is single thread no matter how powerful your machine is and one instance will eat >6GB memory so making run multiple instances also difficult unless you have 128GB something.
...
Forum: Bioinformatics 01-30-2013, 03:47 AM
Replies: 6
Views: 7,741
Posted By xied75
Oh dear, I've no idea if a 32 bit BWA can process...

Oh dear, I've no idea if a 32 bit BWA can process hg19. Anyone?
Forum: Bioinformatics 01-30-2013, 03:40 AM
Replies: 4
Views: 4,262
Posted By xied75
Is your data PE or SE? In fact you can split...

Is your data PE or SE?

In fact you can split BAM directly, no matter compressed or not, it was using bgzip format. I believe there are tools for this.

I would prefer feed BWA BAM files and...
Forum: Bioinformatics 01-30-2013, 03:29 AM
Replies: 13
Views: 3,335
Posted By xied75
Hi, Ole, Not sure about what size will ecSeq...

Hi, Ole,

Not sure about what size will ecSeq provide. In my case I need to run BWA and samtools on Windows so I need at least 4 cores 8GB machine. I use Windows Azure, there is the price...
Forum: Bioinformatics 01-29-2013, 12:55 PM
Replies: 6
Views: 7,741
Posted By xied75
Is this a 64 bit Linux? Did you compile the BWA...

Is this a 64 bit Linux? Did you compile the BWA on it? 680 iterations done, 1892095270 doesn't look correct, it should be 6 billion something. Check your config or make file for 64 bit file access...
Forum: Bioinformatics 01-28-2013, 03:16 AM
Replies: 13
Views: 3,335
Posted By xied75
He means you'll get a Virtual machine image saved...

He means you'll get a Virtual machine image saved for you so that you can start again, with everything still inside. They don't own servers, the Cloud provider does, (e.g. Amazon AWS, Windows Azure),...
Forum: Bioinformatics 01-22-2013, 04:42 AM
Replies: 7
Views: 9,576
Posted By xied75
samtools fixmate

samtools fixmate
Forum: Bioinformatics 01-18-2013, 07:22 AM
Replies: 4
Views: 1,975
Posted By xied75
8:39 you mean 8 mins 39 secs? I/O in this...

8:39 you mean 8 mins 39 secs?

I/O in this case shoudn't be the bottleneck, only a 1.3GB file, cost nothing to read.

Someone familiar with how bowtie2 does the multithreading?

If you like try...
Forum: Bioinformatics 01-17-2013, 10:23 AM
Replies: 7
Views: 1,086
Posted By xied75
Yes it'll confuse the aligner a lot! For the...

Yes it'll confuse the aligner a lot! For the duplicate area, it will need to pick one from the 8. But for variable area, it will report the highest scored one.

For what you want, I guess no...
Forum: Bioinformatics 01-17-2013, 09:36 AM
Replies: 7
Views: 1,086
Posted By xied75
How about join those 8 together as one reference?

How about join those 8 together as one reference?
Showing results 1 to 25 of 129

 


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