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Search: Posts Made By: yasu
Forum: Bioinformatics 03-29-2010, 11:52 PM
Replies: 2
Views: 1,452
Posted By yasu
Hi Colin, Thanks for your quick response!! It...

Hi Colin,
Thanks for your quick response!!
It works well!!
-Yasu
Forum: Bioinformatics 03-29-2010, 10:33 PM
Replies: 2
Views: 1,452
Posted By yasu
novoalign GLIBC error

Hi,

I am going to use novoalign for PE reads and I got the following error message:

$ novoalign -f s_1_1_.fq s_1_2_.fq -d hg19
novoalign: /lib64/libc.so.6: version `GLIBC_2.7' not found...
Forum: Bioinformatics 02-17-2010, 06:28 PM
Replies: 2
Views: 2,481
Posted By yasu
cuffcompare output statistic

I got cuffcompare output something like below:

==================
# Query mRNAs : 250371 in 250079 loci (24778 multi-exon transcripts)
# (282 multi-transcript loci, ~1.0...
Forum: Bioinformatics 02-16-2010, 12:25 AM
Replies: 3
Views: 7,517
Posted By yasu
Thanks, drio!! '$ sudo yum install zlib-devel'...

Thanks, drio!!
'$ sudo yum install zlib-devel' DOES work!!
Forum: Bioinformatics 02-15-2010, 06:37 PM
Replies: 3
Views: 7,517
Posted By yasu
BWA 'make' error

I just want to use BWA-0.5.6 for mapping 454 reads on Linux. I got error message like this;

=========
$ make
make[1]: Entering directory `/home/yago/bwa-0.5.6'
make[1]: Nothing to be done for...
Forum: Bioinformatics 02-08-2010, 11:54 PM
Replies: 4
Views: 2,193
Posted By yasu
I added the '--segment-length 25', but the...

I added the '--segment-length 25', but the comment is still as follows;

[Tue Feb 9 16:47:40 2010] Checking reads
seed length: 43bp
format: fastq
quality scale: --phred33-quals

Did I...
Forum: Bioinformatics 02-08-2010, 11:36 PM
Replies: 4
Views: 2,193
Posted By yasu
Thanks for your kind help!! My fastq file is...

Thanks for your kind help!!

My fastq file is something like this. I omitted the sequence+position id from the line after "+". Does this make the things bad?

-Yasu

###########...
Forum: Bioinformatics 02-08-2010, 10:06 PM
Replies: 4
Views: 2,193
Posted By yasu
I add the report.log file from real_data (failed...

I add the report.log file from real_data (failed one).

### Real_data (reports.log) ###

tophat_reports v1.0.12
---------------------------------------
Error: cannot open map file for reading...
Forum: Bioinformatics 02-08-2010, 02:04 AM
Replies: 4
Views: 2,193
Posted By yasu
Question tophat running problem

Hi all,

I'm trying to run mRNA-seq for human by tophat (v1.0.12).
I succeeded to get proper output file in the preliminary dataset (first 100K reads from each .fq file). But I failed to get...
Forum: Bioinformatics 08-09-2009, 06:34 PM
Replies: 18
Views: 14,860
Posted By yasu
I have a quick question. How can I use 'samtools...

I have a quick question. How can I use 'samtools view' for converting bam file to sam file? I tried some times but I failed to do it...
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