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Forum: Bioinformatics 09-02-2013, 07:40 AM
Replies: 32
Views: 18,882
Posted By middlemale
same problem

I faced the same problem with tophat 2.0.9 (bowtie 2.10.0) for my paired-end rna-seq data.

the size of each file is ~3.6GB, 51 bases, my hardware is 12 core x86 machine with 96GB memory and...
Forum: Bioinformatics 03-12-2013, 05:22 AM
Replies: 2
Views: 723
Posted By middlemale
hi, biznatch. thanks for the quick reply, I...

hi, biznatch.

thanks for the quick reply, I did try table browser, as you suggested, I can get the overlap list from this, or from BEDTools kit.

What we really want to show is the overall...
Forum: Bioinformatics 03-12-2013, 04:27 AM
Replies: 2
Views: 723
Posted By middlemale
visualise co-occupy of a genome with bed files

Hi,

we have some mouse chip-seq data from 4 transcription factors (TFs) that we can look for possible binding sites or target genes for each TF.

Interestingly we found many binding sites...
Forum: Bioinformatics 11-05-2010, 03:44 AM
Replies: 0
Views: 1,204
Posted By middlemale
cuffdiif or cufflinks expr comparisons

hi, I am looking for differentially expressed genes by RNA-seq and used cufflinks for control and test samples.

cufflinks generated **gene.expr files and I assume these files can be used to...
Forum: Bioinformatics 11-05-2010, 03:14 AM
Replies: 26
Views: 13,459
Posted By middlemale
duplicate errors

jb2, I was facing duplicate errors too. In my case , later I run cufflinks without -G option , then that is fine. you may have a try.
Forum: RNA Sequencing 09-24-2010, 01:29 AM
Replies: 2
Views: 1,724
Posted By middlemale
Myrna new reference jar

I am trying to analyse rna-seq data with new Myrna tool locally, which mainly aims to compare the expression differences between control and treated samples.

The question is my species is Danio...
Forum: Bioinformatics 04-13-2010, 02:54 AM
Replies: 10
Views: 9,711
Posted By middlemale
GList.hh:592 error

Same situation for me. I cannot run cuffcompare because of duplicate errors. What I did was to delete all duplicated exon lines (exon numbers vary though) but keep transcript lines with a perl...
Forum: Bioinformatics 04-01-2010, 06:36 AM
Replies: 3
Views: 3,766
Posted By middlemale
thanks gpertea and others. I have tried modifying...

thanks gpertea and others. I have tried modifying genome gtf file from ensembl (like deleting all lines mentioning ENSDART00000099599), but other duplicated IDs are found and there are too many to be...
Forum: RNA Sequencing 03-30-2010, 03:48 AM
Replies: 155
Views: 56,131
Posted By middlemale
thanks xi, I updated R (2.10.1) and DEGseq now ,...

thanks xi, I updated R (2.10.1) and DEGseq now , but the errors are the same
"Error in DEGexp(geneExpMatrix1 = geneExpMatrix1, geneCol1 = 1, expCol1 = c(2, :
unused argument(s) (geneExpMatrix1...
Forum: RNA Sequencing 03-29-2010, 08:54 AM
Replies: 155
Views: 56,131
Posted By middlemale
unused arguments error (DEGseq)

I tried DEGexp in R with example data, but got error "Error in DEGexp(geneExpMatrix1 = geneExpMatrix1, geneCol1 = 1, expCol1 = c(2, :
unused argument(s) (geneExpMatrix1 = geneExpMatrix1,...
Forum: Bioinformatics 03-22-2010, 08:36 AM
Replies: 6
Views: 3,150
Posted By middlemale
possibly your sam file requires sorted by...

possibly your sam file requires sorted by samtools . I did not have experience. good luck.
Forum: Bioinformatics 03-18-2010, 04:53 AM
Replies: 3
Views: 3,766
Posted By middlemale
cufflinks errors of duplicates

Hi,

I searched for a while for my problem running cufflinks, sounds no answer yet.

I run tophat + bowtie for RNA-seq data (single end read), and got the widetype .sam file plus treated .sam...
Forum: Bioinformatics 03-15-2010, 10:13 AM
Replies: 5
Views: 1,553
Posted By middlemale
in my case, single end read and I try to use gene...

in my case, single end read and I try to use gene model annotation
tophat -G <GFF3 file> /path/to/indices fastq_file

same problem "Error: you must set the mean inner distance between mates with...
Forum: Bioinformatics 03-09-2010, 08:44 AM
Replies: 23
Views: 22,634
Posted By middlemale
Excellent. many thanks . much clear for me now.

Excellent. many thanks . much clear for me now.
Forum: Bioinformatics 03-09-2010, 07:24 AM
Replies: 23
Views: 22,634
Posted By middlemale
Hi, by chance can anybody clarify my confusion...

Hi, by chance can anybody clarify my confusion about cuffdiff.

the input for cufdiff is <transcripts.gtf> and 2 or more sam files. in my case, there are 2 transcripts gtf files (s_7.gtf for...
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