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Search: Posts Made By: victoryhe
Forum: Bioinformatics 12-13-2011, 11:42 AM
Replies: 0
Views: 1,482
Posted By victoryhe
microRNA -- alignment

Post allignment of microRNA and mapping against Mirbase I have a column ID with the precursor as well as the mature microRNA name, on parsing the column I have the list with the mature microRNA which...
Forum: Bioinformatics 11-09-2011, 05:22 AM
Replies: 0
Views: 1,436
Posted By victoryhe
A question on cisgenome

Dear All,

I am running cisgenome to identify known motif mapping of chipseq TF data on Windows GUI. Using one motif matrix and mm9 mouse Genome data base, If i run cisgenome for known motif...
Forum: Bioinformatics 10-18-2011, 05:00 AM
Replies: 1
Views: 1,412
Posted By victoryhe
cufflinks

Hi,

i'm getting Read type 0bp singled-end in the output of cufflinks, even it is 75bp. And, In the gene.fpkm/isoform file, it has lots of zero counts.

$ cufflinks -o /cufflinks/ -p 4 -g ...
Forum: Bioinformatics 10-17-2011, 12:30 PM
Replies: 3
Views: 1,400
Posted By victoryhe
not small RNA, i am taking a look at RNA-Seq...

not small RNA, i am taking a look at RNA-Seq data. for this, rFAM is better, right? anything else?
Forum: Bioinformatics 10-17-2011, 06:09 AM
Replies: 3
Views: 1,400
Posted By victoryhe
noncoding RNAs

Hi,

how can i get how many transcripts map to rRNA genes, tRNA, snoRNA, microRNA, lincs ,etc, respectively? manually do i count them? is there any tool or package to do it?

any tips would be...
Forum: Bioinformatics 10-17-2011, 05:53 AM
Replies: 2
Views: 7,116
Posted By victoryhe
thanks! without the solexa option, it works.

thanks! without the solexa option, it works.
Forum: Bioinformatics 10-12-2011, 11:18 AM
Replies: 2
Views: 7,116
Posted By victoryhe
Unhappy tophat Error running running 'prep_reads'

Hi, Naive here, i'm getting an error from tophat with mac os x 10.6


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tophat -o /tophatoutput/ --solexa1.3-quals /bowtie-0-1.12.7/indexes/mm9 a.fastq

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