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Search: Posts Made By: libiyagirl
Forum: Bioinformatics 03-28-2012, 02:23 PM
Replies: 3
Views: 1,532
Posted By libiyagirl
Euler2 installing problem

Anyone have tried Euler2 for assembly? When I was installing it, I got errors:

gcc -Iinc/ -c g_band.c
g_band.c:44: error: static declaration of 'g' follows non-static declaration...
Forum: Bioinformatics 03-06-2012, 12:05 PM
Replies: 147
Views: 59,021
Posted By libiyagirl
Hi Kai, I found that the bam_configuration...

Hi Kai,

I found that the bam_configuration method takes different number of reads for analysis, compared with the bam2pindel.pl method. Could you please explain it to me? And the new version,...
Forum: Bioinformatics 02-21-2012, 02:30 PM
Replies: 147
Views: 59,021
Posted By libiyagirl
Hey Kai, I am just wondering about the power...

Hey Kai,

I am just wondering about the power of Pindel to detect long insertions. When I was running Pindel on a single chromosome, I didn't find any large insertions. But actually there are some...
Forum: Bioinformatics 07-19-2011, 08:30 AM
Replies: 2
Views: 2,340
Posted By libiyagirl
software that finding gene fusions on exome sequencing?

Hi all,

I'm thinking using exome sequencing data to look at gene fusions or larger indels. Does anyone know which software is good for this? I know it's going to be difficult because most...
Forum: Bioinformatics 07-05-2011, 02:39 PM
Replies: 1
Views: 1,611
Posted By libiyagirl
driver identification using CHASM in cancer

Hello,

I am trying to run CHASM "BuildClassifier" command. But it always return error saying:

Traceback (most recent call last):
File "<string>", line 31, in <module>
File...
Forum: Bioinformatics 03-07-2011, 03:10 PM
Replies: 5
Views: 2,830
Posted By libiyagirl
Hey I merged all the windows from dindel into a...

Hey I merged all the windows from dindel into a single bam file using samtools merge command. But I didn't check if there's any overlapping windows. Do you always have this problem?
Forum: Bioinformatics 03-04-2011, 12:27 PM
Replies: 5
Views: 2,529
Posted By libiyagirl
Thank you all, I used ...

Thank you all, I used
input="$PATH/sorted.bam";
and it's working now!

Thanks a lot~!
Forum: Bioinformatics 03-03-2011, 04:11 PM
Replies: 5
Views: 2,529
Posted By libiyagirl
Thank you Michael, it seems like chmod 755 can...

Thank you Michael, it seems like chmod 755 can not change the permission of input.bam
Any solution?
Forum: Bioinformatics 03-03-2011, 03:33 PM
Replies: 5
Views: 2,529
Posted By libiyagirl
can I automate running dindel?

Hello,

I am writing a script for automatically running dindel commands. But it never works.

For example, whenever I use:
"input_file=/path/input_file.bam
dindel --bamFile $input_file"

it...
Forum: Bioinformatics 02-07-2011, 07:35 AM
Replies: 2
Views: 2,507
Posted By libiyagirl
Any one has any idea?

Any one has any idea?
Forum: Bioinformatics 02-04-2011, 08:54 AM
Replies: 2
Views: 2,507
Posted By libiyagirl
Using Dindel: callback and output on realigned BAM

Hello, when I'm using dindel, I want to output the realigned BAM file for the genome viewer. So I used the option --outputRealignedBAM, and then I had many many files. Is it possible that I merge all...
Forum: Bioinformatics 02-04-2011, 07:33 AM
Replies: 3
Views: 2,309
Posted By libiyagirl
Hi Fitzgeraldlm, thank you very much for the...

Hi Fitzgeraldlm, thank you very much for the tips! Currently my supervisor wanna me try Dindel first, but I'm sure I will use GATK soon.
Forum: Bioinformatics 02-03-2011, 11:35 AM
Replies: 3
Views: 2,309
Posted By libiyagirl
I have the same question. Any idea?

I have the same question. Any idea?
Forum: Bioinformatics 01-31-2011, 08:24 AM
Replies: 7
Views: 3,354
Posted By libiyagirl
Hello, problem solved! It was funny because I...

Hello, problem solved! It was funny because I basically typed the same thing! But this time it's working. Big thanks!
Forum: Bioinformatics 01-31-2011, 08:00 AM
Replies: 7
Views: 3,354
Posted By libiyagirl
hi gaffa, thank you very much for your...

hi gaffa,

thank you very much for your reply. however, regarding stage 4, the problem is still not solved. so I created a file run1_outputfiles.txt, with the following lines:
...
Forum: Bioinformatics 01-28-2011, 01:51 PM
Replies: 7
Views: 3,354
Posted By libiyagirl
another stupid question about dindel

Hello, I'm running the stage 3 of dindel now. On stage 2 it generated hundreds realign_window.n.txt files. Does it mean I have to run all of them on stage 3 to get hundreds of the...
Forum: Bioinformatics 01-28-2011, 11:45 AM
Replies: 30
Views: 10,634
Posted By libiyagirl
Please ignore my message, problem solved!

Please ignore my message, problem solved!
Forum: Bioinformatics 01-28-2011, 11:39 AM
Replies: 30
Views: 10,634
Posted By libiyagirl
In my case, when I was running $ python ...

In my case, when I was running

$ python makeWindows.py --inputVarFile 1.txt --windowFileFrefix sample.realign_windows--numWindowsPerFile 1000

it says I should specify --windowFilePrefix
why?...
Forum: Bioinformatics 01-28-2011, 09:58 AM
Replies: 12
Views: 3,376
Posted By libiyagirl
Problem solved! The thing was I did not put the...

Problem solved! The thing was I did not put the path to the file. But now it works. Thank you!
Forum: Bioinformatics 01-28-2011, 08:45 AM
Replies: 12
Views: 3,376
Posted By libiyagirl
Thank you very much. I installed the program and...

Thank you very much. I installed the program and now I can use it properly. But still, the first command seems not working. So I used BAM file and FA file, but it said build FASTA index, open: no...
Forum: Bioinformatics 01-27-2011, 06:36 PM
Replies: 7
Views: 5,594
Posted By libiyagirl
it said make: command not found. I also typed...

it said make: command not found. I also typed ./samtools it said no such directory!
Forum: Bioinformatics 01-27-2011, 05:58 PM
Replies: 7
Views: 5,594
Posted By libiyagirl
hello when I extracted samtools, I typed cd...

hello when I extracted samtools, I typed cd samtools-0.1.12a, then it went to the directory. Then I typed $ make samtools, it didn't work. How to install samtools anyway?

Thank you!
Forum: Bioinformatics 01-27-2011, 02:20 PM
Replies: 12
Views: 3,376
Posted By libiyagirl
Hi thank you very much for your files. They are...

Hi thank you very much for your files. They are very helpful. I'm pretty sure I installed dindel already, but I will double check. Thank you very much for your help!
Forum: Bioinformatics 01-27-2011, 02:00 PM
Replies: 12
Views: 3,376
Posted By libiyagirl
I also typed $ ./dindel_x86-64, it also said...

I also typed $ ./dindel_x86-64, it also said command not found.....
Forum: Bioinformatics 01-27-2011, 01:49 PM
Replies: 12
Views: 3,376
Posted By libiyagirl
I mean in unix when I type dindel, it just says...

I mean in unix when I type dindel, it just says no such command.
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