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Search: Posts Made By: Ms@New
Forum: Bioinformatics 08-16-2010, 04:29 PM
Replies: 2
Views: 1,599
Posted By Ms@New
thanks for the quick response. I still have...

thanks for the quick response.

I still have some questions,
In my case, --best is almost always faster.

may be I'm wrong, but as I remember, --best option finds the best match for the read,...
Forum: Bioinformatics 08-16-2010, 03:51 PM
Replies: 2
Views: 1,599
Posted By Ms@New
question about bowtie result and time

Hi,

I am running bowtie on a set of reads.

my problem is when I use option --best, it takes less time than default option. but I think it should take more time.

another problem is, when I...
Forum: Bioinformatics 08-16-2010, 01:45 PM
Replies: 2
Views: 1,574
Posted By Ms@New
thanks adam

thanks adam
Forum: Bioinformatics 08-12-2010, 08:16 AM
Replies: 2
Views: 1,574
Posted By Ms@New
maq output

Hi,

I want to have a distribution of number of mismatches in mapped reads from .map file. (how many of mapped reads have 1 mismatch, how may have 2, etc.)

it's a straight forward question, I'm...
Forum: Bioinformatics 08-12-2010, 04:24 AM
Replies: 5
Views: 3,263
Posted By Ms@New
Hi, I get the same error, and I'm using hg18...

Hi, I get the same error, and I'm using hg18 index from bowtie website.

Did you figure out what was the problem?
Forum: Bioinformatics 08-10-2010, 01:02 PM
Replies: 4
Views: 1,307
Posted By Ms@New
Thanks, I have a couple of dump questions, I...

Thanks,

I have a couple of dump questions, I think I'm lost in SRA.

for example, in one entry, in description part it says :

a 200 bp insert size means the distance between paired reads is...
Forum: Bioinformatics 08-03-2010, 12:25 PM
Replies: 4
Views: 1,307
Posted By Ms@New
thanks, but I want to be able to get a consensus...

thanks, but I want to be able to get a consensus sequence, and if I choose a small subset of human reads, there won't be enough coverage.

Thanks
Forum: Bioinformatics 08-03-2010, 11:20 AM
Replies: 4
Views: 1,307
Posted By Ms@New
data for Maq

Hi everyone,

I'm looking for some real , not very big data to run maq. (preferably paired-end reads)

I found some human sample reads, but they are huge, and I want to run maq on a relatively...
Forum: Bioinformatics 07-29-2010, 08:15 AM
Replies: 5
Views: 5,030
Posted By Ms@New
Hi, I have a question about bowtie index, I...

Hi,

I have a question about bowtie index, I though this is the right forum to post it.

What exactly bowtie indexes?
I've read :

BWT (same size as T)
Checkpoints (~15% size of T)
SA sample...
Forum: Bioinformatics 07-22-2010, 06:21 AM
Replies: 17
Views: 3,608
Posted By Ms@New
Thanks for the reply I downloaded the files...

Thanks for the reply
I downloaded the files from the link you provided, but I have trouble running it.

in the cloudmaq.sh, there is

$HADOOP_HOME/bin/hadoop jar...
Forum: Bioinformatics 07-21-2010, 07:51 PM
Replies: 50
Views: 22,381
Posted By Ms@New
Hi everyone, I'm trying to install maqview,...

Hi everyone,

I'm trying to install maqview, but I get the

I have the same problem
view_panel.o: In function `resetPickMatrixs':...
Forum: Bioinformatics 07-21-2010, 05:40 PM
Replies: 17
Views: 3,608
Posted By Ms@New
Hi, does it still works with MAQ 0.6.8 ? ...

Hi,

does it still works with MAQ 0.6.8 ?

I'm new to the field, and I wanted to run it on IBM clusters. This seems to be the solution. is source code available?

does anyone know if the...
Forum: Bioinformatics 06-30-2010, 09:04 PM
Replies: 12
Views: 2,916
Posted By Ms@New
Hi R_diggy, I have the same problem, Could you...

Hi R_diggy, I have the same problem,
Could you let me know if it was solved after doing


Thanks for the help Raela :)
Forum: Bioinformatics 06-29-2010, 11:17 AM
Replies: 12
Views: 2,916
Posted By Ms@New
I commented out the simustat line, and it runs...

I commented out the simustat line, and it runs now.

I'll try it on a 64 bit to see if that solves the problem or not.

thanks for your help.
Forum: Bioinformatics 06-29-2010, 07:56 AM
Replies: 12
Views: 2,916
Posted By Ms@New
Thanks for your reply, I'm running on a 32...

Thanks for your reply,

I'm running on a 32 bit.

I've downloaded calib.data, and found a bacterial genome. but after I got the buffer overflow, I decreased size of ref.fasta, and number of...
Forum: Bioinformatics 06-28-2010, 04:07 PM
Replies: 12
Views: 2,916
Posted By Ms@New
I get the buffer overflow when it wants to run ...

I get the buffer overflow when it wants to run
usr/local/bin/maq simustat easyrun/all.map > eval.simustat
Forum: Bioinformatics 06-28-2010, 01:51 PM
Replies: 12
Views: 2,916
Posted By Ms@New
Hi yuanlang, Were you able to solve your...

Hi yuanlang,

Were you able to solve your problem?
I tried to run Maq's demo, but I ran to the same problem, right now,. I use a VERY small sequence, and I decreased number of simulated reads,...
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