Forum: Bioinformatics
03-28-2012, 01:23 PM
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Replies: 3
Views: 1,562
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...
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Forum: Bioinformatics
03-06-2012, 11:05 AM
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Replies: 147
Views: 59,774
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,...
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Forum: Bioinformatics
02-21-2012, 01:30 PM
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Replies: 147
Views: 59,774
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...
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Forum: Bioinformatics
07-19-2011, 07:30 AM
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Replies: 2
Views: 2,390
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Forum: Bioinformatics
07-05-2011, 01:39 PM
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Replies: 1
Views: 1,648
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...
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Forum: Bioinformatics
03-07-2011, 02:10 PM
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Replies: 5
Views: 2,887
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Forum: Bioinformatics
03-04-2011, 11:27 AM
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Replies: 5
Views: 2,601
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Forum: Bioinformatics
03-03-2011, 03:11 PM
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Replies: 5
Views: 2,601
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Forum: Bioinformatics
03-03-2011, 02:33 PM
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Replies: 5
Views: 2,601
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...
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Forum: Bioinformatics
02-07-2011, 06:35 AM
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Replies: 2
Views: 2,592
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Forum: Bioinformatics
02-04-2011, 07:54 AM
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Replies: 2
Views: 2,592
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...
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Forum: Bioinformatics
02-04-2011, 06:33 AM
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Replies: 3
Views: 2,360
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Forum: Bioinformatics
02-03-2011, 10:35 AM
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Replies: 3
Views: 2,360
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Forum: Bioinformatics
01-31-2011, 07:24 AM
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Replies: 7
Views: 3,415
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Forum: Bioinformatics
01-31-2011, 07:00 AM
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Replies: 7
Views: 3,415
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:
...
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Forum: Bioinformatics
01-28-2011, 12:51 PM
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Replies: 7
Views: 3,415
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...
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Forum: Bioinformatics
01-28-2011, 10:45 AM
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Replies: 30
Views: 10,829
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Forum: Bioinformatics
01-28-2011, 10:39 AM
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Replies: 30
Views: 10,829
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?...
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Forum: Bioinformatics
01-28-2011, 08:58 AM
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Replies: 12
Views: 3,448
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Forum: Bioinformatics
01-28-2011, 07:45 AM
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Replies: 12
Views: 3,448
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Forum: Bioinformatics
01-27-2011, 05:36 PM
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Replies: 7
Views: 5,649
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Forum: Bioinformatics
01-27-2011, 04:58 PM
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Replies: 7
Views: 5,649
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Forum: Bioinformatics
01-27-2011, 01:20 PM
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Replies: 12
Views: 3,448
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Forum: Bioinformatics
01-27-2011, 01:00 PM
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Replies: 12
Views: 3,448
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Forum: Bioinformatics
01-27-2011, 12:49 PM
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Replies: 12
Views: 3,448
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