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Search: Posts Made By: Triple_W
Forum: Bioinformatics 09-02-2013, 06:34 AM
Replies: 0
Views: 1,576
Posted By Triple_W
Wink Interesting: about the names of cufflinks, tophat and bowtie

I am just curious why the authors gave their software names of bowtie, tophat and cufflinks, respectively.
Forum: Bioinformatics 07-03-2013, 12:48 AM
Replies: 1
Views: 1,416
Posted By Triple_W
can cuffdiff handle the samples with different treatments and a time series?

Hi friends,
Recently, I got a problem, I have two treated samples, one is KO, and the other is WT (as control), and the two samples also have a time series. In other words, I have four sequencing...
Forum: Bioinformatics 07-03-2013, 12:44 AM
Replies: 1
Views: 1,176
Posted By Triple_W
Forum: Bioinformatics 05-24-2013, 01:51 AM
Replies: 1
Views: 1,176
Posted By Triple_W
Tophat result: how to get the number for novel junctions

hi,

tophat can output a file junctions.bed including the splicing sites for junction reads.
Can I get novel splicing sites that tophat identified from known ones given by reference gene...
Forum: Bioinformatics 05-16-2013, 07:07 PM
Replies: 7
Views: 4,304
Posted By Triple_W
I also met the error, anyone solved it? ...

I also met the error, anyone solved it?
[2013-05-17 02:36:07] Mapping left_kept_reads to transcriptome genes with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read:...
Forum: Bioinformatics 02-24-2013, 06:05 PM
Replies: 5
Views: 3,730
Posted By Triple_W
Tophat error running from bam2fastx?

Hi,
I just used TopHat v2.0.6 and came cross the following error


[2013-02-23 15:02:48] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-02-23 15:02:48]...
Forum: Bioinformatics 12-25-2012, 06:16 PM
Replies: 3
Views: 1,442
Posted By Triple_W
I cannot download your "gff" file, can you paste...

I cannot download your "gff" file, can you paste some head lines?
Forum: Bioinformatics 12-25-2012, 04:31 AM
Replies: 3
Views: 1,442
Posted By Triple_W
If you are familar with perl. I think the script...

If you are familar with perl. I think the script ucsc_table2gff3.pl from biotoolbox can solve your problem.
see http://code.google.com/p/biotoolbox/
Forum: Bioinformatics 11-27-2012, 06:44 PM
Replies: 10
Views: 7,307
Posted By Triple_W
Smile The information is helpful. Does tophat in Galaxy...

The information is helpful. Does tophat in Galaxy adopt such protocal?

However, I found .bam file from tophat.v2 used a different version:
255: unmapped reads
50: unique mapped reads
3: two...
Forum: Bioinformatics 01-11-2012, 06:47 PM
Replies: 2
Views: 3,423
Posted By Triple_W
Thanks very much for your response. it is...

Thanks very much for your response. it is helpful.
What do you think about the following strategy?
When the percentage of mapped unique reads is low (e.g 40%~50%), we can consider randomly...
Forum: Bioinformatics 01-10-2012, 07:56 PM
Replies: 2
Views: 3,423
Posted By Triple_W
what should i do with multiple mapped reads ?

I am new in ChIP-seq data analysis, and I have a question.
As you know, some reads often have >=2 valid alignments in genome reference. I see some authors liked to discard these un-uniquely mapped...
Forum: Bioinformatics 01-09-2012, 12:49 AM
Replies: 0
Views: 1,962
Posted By Triple_W
Red face bowtie 2 on win7 bits32 installation?

When i install bowtie 2 by Cygwin (on win7 32 bits), the problem occured in the following:



/usr/bin/g++ -O3 -m32 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m32 -msse2 -funroll-loops...
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