SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 23 of 23
Search took 0.02 seconds.
Search: Posts Made By: Hunny
Forum: Bioinformatics 07-04-2012, 06:34 PM
Replies: 0
Views: 1,437
Posted By Hunny
Post Unknown definitions of instances output by CummeRbund

Hi all,

Now I am trying to analyze the results of differential expression tests using CummeRbund. I simply loaded the output files of Cuffdiff into CummeRbund. And I got some basic statistics as...
Forum: Bioinformatics 06-27-2012, 10:34 PM
Replies: 3
Views: 1,609
Posted By Hunny
No, I gave it up. Thank you for your...

No, I gave it up.


Thank you for your trying. However, I intended to run Scripture for all chromosomes. It seems a little bit trivial to run with -chr and -chrSequence parameters for all...
Forum: Bioinformatics 06-07-2012, 12:50 AM
Replies: 3
Views: 1,609
Posted By Hunny
Wink Scripture collapsed when assemling read alignments

Hi :),

When I am using Scripture(scripture-beta2.jar) to assemble read alignmets, the program collapsed with following output



What I did previously include

--Generated accepted_hits.bam...
Forum: Bioinformatics 05-24-2012, 05:31 PM
Replies: 2
Views: 1,184
Posted By Hunny
It seems the problem can be fixed by updating...

It seems the problem can be fixed by updating tophat.
See http://tophat.cbcb.umd.edu/
Forum: Bioinformatics 10-04-2011, 02:46 AM
Replies: 20
Views: 5,249
Posted By Hunny
I am working with Illumina single-end reads. ...

I am working with Illumina single-end reads.
No, I didn't specify a library type, just with default options.

Cheers,
Forum: Bioinformatics 10-03-2011, 05:42 PM
Replies: 20
Views: 5,249
Posted By Hunny
Hi avi, Yes, I see. I've just now...

Hi avi,



Yes, I see. I've just now checked my predicted transcripts from Cufflinks. And I find that Cufflinks does not assign any strand information on some of my single-exon...
Forum: Bioinformatics 09-30-2011, 02:23 AM
Replies: 20
Views: 5,249
Posted By Hunny
I am wondering how you could know some assigned...

I am wondering how you could know some assigned strands is wrong. Have you got reference transcripts for them?
Forum: Bioinformatics 09-30-2011, 02:11 AM
Replies: 20
Views: 5,249
Posted By Hunny
I don't know if I have catched your meaning. ...

I don't know if I have catched your meaning.
But I guess it depends on which strand is defined "sense" or "antisense". I think it is reasonable to assign "+" to an "antisense" strand. You can check...
Forum: Bioinformatics 09-30-2011, 01:55 AM
Replies: 20
Views: 5,249
Posted By Hunny
I think assigning a strand for a transcript...

I think assigning a strand for a transcript depends on which genome sequence on which the reads are mapping. The strand should be + if reads are mapped on the sense strand, and vice versa.

Cheers,
Forum: Bioinformatics 09-30-2011, 12:37 AM
Replies: 10
Views: 3,780
Posted By Hunny
Post Hi, I have been reading the supplemental...

Hi,

I have been reading the supplemental material of Cufflinks.
And I have been hurt by the lots of formulas on it.:(
Could you tell me the reason why they use the adjusted length? What does the...
Forum: Bioinformatics 09-09-2011, 04:00 AM
Replies: 13
Views: 11,021
Posted By Hunny
Hi Jane, Your Cuffdiff output printing is...

Hi Jane,

Your Cuffdiff output printing is actually normal !


This sentence is printed before all processes below.


The first half block above might be for your first condition sample.
And...
Forum: Bioinformatics 09-08-2011, 05:54 PM
Replies: 13
Views: 11,021
Posted By Hunny
Hi Jane, I also encounter this problem...

Hi Jane,



I also encounter this problem when running Cuffdiff on 2 condition samples (3 replicates for each). But my output is an another variant, which "Inspecting maps and determining...
Forum: Bioinformatics 09-08-2011, 05:20 AM
Replies: 13
Views: 11,021
Posted By Hunny
Wierd. I suggest you could use the latest...

Wierd.
I suggest you could use the latest release Cufflinks-1.0.3 package and run it again.

Good luck!
Forum: Bioinformatics 07-22-2011, 03:07 AM
Replies: 15
Views: 11,931
Posted By Hunny
I guess you need to export the path of samtools...

I guess you need to export the path of samtools to your shell PATH, just using a command like
$ export PATH=/your_samtools_directory/:$PATH

or you can insert the command above in your...
Forum: Bioinformatics 06-01-2011, 05:36 AM
Replies: 7
Views: 4,550
Posted By Hunny
I have a question here. As mentioned in the...

I have a question here.

As mentioned in the mannul of cufflinks, "Output will include all reference transcripts as well as any novel genes and isoforms that are assembled." is for the...
Forum: Bioinformatics 05-24-2011, 09:19 PM
Replies: 9
Views: 20,206
Posted By Hunny
Well, many facts manifest that the higher the...

Well, many facts manifest that the higher the value, the better the alignment with 255 of its maximum. So, I guess "mapping quality is not available" means the value 255 is meaningless for such a...
Forum: Bioinformatics 05-24-2011, 07:52 PM
Replies: 9
Views: 20,206
Posted By Hunny
Hi, I have the same problem when aligning...

Hi,

I have the same problem when aligning reads using Tophat.

The values in my sam file generated by tophat range from 0 to 255, which is different from your example.

I look up the field...
Forum: Bioinformatics 05-10-2011, 07:53 PM
Replies: 31
Views: 12,427
Posted By Hunny
Hi Cole, On the manual of cufflinks ...

Hi Cole,

On the manual of cufflinks
http://cufflinks.cbcb.umd.edu/manual.html#gtfout

One option of cuffmerge should be -g/--ref-gtf, not -r/--ref-gtf showed on current website,
right?
...
Forum: Bioinformatics 05-09-2011, 05:10 PM
Replies: 0
Views: 2,388
Posted By Hunny
One problem about RefSeq annotation file

Hi Guys,

I have one question about the RefSeq annotation file downed from UCSC.

Take the mm9 as example,

Firstly, I downloaded the RefSeq GTF file of mm9 genome from the UCSC website and...
Forum: Bioinformatics 04-28-2011, 09:33 PM
Replies: 0
Views: 3,742
Posted By Hunny
Minimum hardware requirements for TopHat

Hi,

Does anyone know the minimum hardware, such as CPU, RAM and disk, requirements for running TopHat on a RNA-Seq dataset with a size of >25 million reads?

Thanks.
Forum: Bioinformatics 04-18-2011, 05:21 PM
Replies: 5
Views: 1,988
Posted By Hunny
Hi, Thank you again! I have downloaded the...

Hi,

Thank you again! I have downloaded the data from their website successfully!

Since I want to test TopHat using a real dataset, I also need a reference genome for mapping the RNA-Seq data...
Forum: Bioinformatics 04-18-2011, 04:05 PM
Replies: 5
Views: 1,988
Posted By Hunny
Thank you so much. I will check it :)

Thank you so much. I will check it :)
Forum: Bioinformatics 04-18-2011, 03:38 PM
Replies: 5
Views: 1,988
Posted By Hunny
Where could I get a set of real RNA-Seq data

Hello guys!

I would like to know where I could get a set of real RNA-Seq data.

I've searched many papers about RNA-Seq, but I haven't found any one providing RNA-Seq data.

Thanks :)
Showing results 1 to 23 of 23

 


All times are GMT -8. The time now is 11:03 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO