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Forum: RNA Sequencing 01-27-2013, 07:17 PM
Replies: 0
Views: 1,526
Posted By masterpiece
Exonerate: filter low quality hits

hi Seqanswer,

We have transcriptome data assembled using de-novo assembly approach. Recently, we have genome sequence available, therefore we decided to map the assembled transcripts to genome...
Forum: Genomic Resequencing 11-30-2012, 02:39 AM
Replies: 3
Views: 2,463
Posted By masterpiece
You cannot run tophat 1.4 with Bowtie2. You have...

You cannot run tophat 1.4 with Bowtie2. You have to install Tophat version 2.0.* if you want to use Bowtie2.

kamal
Forum: Bioinformatics 11-01-2012, 08:00 PM
Replies: 8
Views: 4,536
Posted By masterpiece
Can you share with us the command you use to run...

Can you share with us the command you use to run the cuffdiff ?
Forum: Bioinformatics 10-16-2012, 09:02 PM
Replies: 2
Views: 3,435
Posted By masterpiece
Did you run cuffdiff with '\' in the command?...

Did you run cuffdiff with '\' in the command? Remove the '\', leave a space between the 2 samples and run the command
Forum: Bioinformatics 10-15-2012, 06:57 PM
Replies: 8
Views: 11,165
Posted By masterpiece
Hi Blanco, Sorry for late reply. Busy with...

Hi Blanco,

Sorry for late reply. Busy with other stuff lately.

This is human transcriptome dataset from ENCODE/Cold Spring Harbor Lab. They done a lot of RNAseq sequencing. You can check their...
Forum: Bioinformatics 10-15-2012, 06:42 PM
Replies: 6
Views: 3,340
Posted By masterpiece
JackieBadger, Nowdays, more and more...

JackieBadger,

Nowdays, more and more universities required student to publish at least a paper as a requirement for the student to graduate. Same thing happen in a lot of places, for example in...
Forum: Bioinformatics 10-11-2012, 07:26 PM
Replies: 8
Views: 11,165
Posted By masterpiece
Hi Blanco, We've tried rseqc to check on...

Hi Blanco,

We've tried rseqc to check on the library type for our RNAseq data. But the package doesn't have much details about the output.

Here is our results

Fraction of reads explained by...
Forum: Bioinformatics 09-27-2012, 10:30 PM
Replies: 21
Views: 5,662
Posted By masterpiece
vinay052003, As far I know, you can't use...

vinay052003,

As far I know, you can't use cuffdiff output to be used in DEseq run. You have to start from bam files generated by tophat and run through Htseq-count and DEseq

tophat ->...
Forum: Bioinformatics 09-27-2012, 07:34 PM
Replies: 16
Views: 12,171
Posted By masterpiece
About the tview, from the way you run the...

About the tview, from the way you run the command, I think u missed something. Have you sort the bam file using samtool sort command? If not, you have to sort them 1st, before doing indexing.

...
Forum: Bioinformatics 09-27-2012, 01:14 AM
Replies: 16
Views: 12,171
Posted By masterpiece
As what dpryan and other said, its the header...

As what dpryan and other said, its the header issue. May I know how you generate the sam file at the first place?
Forum: Sample Prep / Library Generation 09-26-2012, 07:49 PM
Replies: 11
Views: 9,958
Posted By masterpiece
I found this recently published paper discussion...

I found this recently published paper discussion on effect on transcripts detection after globin removal. Might be useful to you guys.
http://www.biomedcentral.com/content/pdf/1471-2164-13-28.pdf
...
Forum: Bioinformatics 09-24-2012, 11:28 PM
Replies: 21
Views: 5,662
Posted By masterpiece
billstevens Unfortunately I don't think I...

billstevens

Unfortunately I don't think I can help you on this. My task is generating results from sequence reads, run the statistics analysis. Later i pass them to other person in our lab for...
Forum: Bioinformatics 09-24-2012, 11:13 PM
Replies: 17
Views: 13,822
Posted By masterpiece
Hi there, I'm not a statistician, so I can't...

Hi there,

I'm not a statistician, so I can't answer you how the software count the p-value. But I can suggest you reads this thread http://seqanswers.com/forums/newreply.php?do=newreply&p=83270 (...
Forum: Bioinformatics 09-23-2012, 04:00 AM
Replies: 21
Views: 5,662
Posted By masterpiece
May I know do you have replicates in your...

May I know do you have replicates in your analysis. Without replicates, the statistics shown will not be strong enough to support your results.

Normally in my case, apart from using p-value or...
Forum: Bioinformatics 09-22-2012, 02:44 PM
Replies: 21
Views: 5,662
Posted By masterpiece
Bill Steven, Yup, I did tried using the...

Bill Steven,

Yup, I did tried using the DESeq for analysis and I prefer the way it report the results compared to cuffdiff. They report out "variation between replicates", which is not provided in...
Forum: Bioinformatics 09-05-2012, 09:06 PM
Replies: 21
Views: 5,662
Posted By masterpiece
sqcrft Apology for late reply due to busy...

sqcrft

Apology for late reply due to busy with other project.

I've tried run according to your suggestion, but the problem still there. No luck I think. Well I think at the moment I just focus...
Forum: Bioinformatics 08-03-2012, 02:31 AM
Replies: 21
Views: 5,662
Posted By masterpiece
Yes, I'm using different gtf files as the...

Yes, I'm using different gtf files as the cuffdiff required for me to combined the gtf files by using the cuffmerge command. But technically both gtf files (combined.gtf and cuffcmp.combined.gtf )...
Forum: Bioinformatics 08-01-2012, 11:52 PM
Replies: 21
Views: 5,662
Posted By masterpiece
Hmm... I've tried rerun the same command using...

Hmm... I've tried rerun the same command using cufflink version 2.02 (previously version 2.01), however the problem still remain :( . At the moment I'm using the approach that I mentioned above
...
Forum: Bioinformatics 08-01-2012, 01:07 AM
Replies: 21
Views: 5,662
Posted By masterpiece
Great!, I thought I was the only person who got...

Great!, I thought I was the only person who got this problem. Bad thing is, I haven't solved the problem yet, but at the moment I just use results from cufflinks run as I looking into differential...
Forum: Bioinformatics 06-29-2012, 03:00 AM
Replies: 21
Views: 5,662
Posted By masterpiece
inconsistancy between cufflinks and cuffdiffs output?

Hi all,

I'm working on differential expression analysis on bacterial transcriptome using cufflinks packages. However I found these result (table below) that confusing me. Some of the expression...
Forum: RNA Sequencing 06-08-2012, 10:11 PM
Replies: 1
Views: 4,640
Posted By masterpiece
Have you tried using the BAM files instead of the...

Have you tried using the BAM files instead of the sorted SAM files. I settled mine using the BAM files
Forum: RNA Sequencing 06-08-2012, 02:18 AM
Replies: 17
Views: 16,389
Posted By masterpiece
I'm afraid only the Tophat develop can answer this

I'm afraid only the Tophat develop can answer this
Forum: RNA Sequencing 05-23-2012, 09:28 PM
Replies: 17
Views: 16,389
Posted By masterpiece
Thanks for the tips, but how about for paired...

Thanks for the tips, but how about for paired reads dataset? The sam file don't keep the paired read information (/1 and /2). I think calculating using 'sort and uniq' may not be correct if broken...
Forum: RNA Sequencing 04-05-2012, 07:49 PM
Replies: 0
Views: 2,924
Posted By masterpiece
cufflinks : difference in --GTF and --GTF-guide result

Hi all,


I've run transcriptome data analysis on bacteria samples. However, I'm puzzle on expression result differences between --GTF and --GTF-guide option used when run cufflinks. All...
Forum: De novo discovery 11-25-2011, 03:13 AM
Replies: 1
Views: 1,718
Posted By masterpiece
to complete or not to complete

Hi guys,

I want to get opinion from you all. For some of us might think completing a genome assembly (in this case sample from microbe) might be easy. But for some of us with limited of experience...
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