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Search: Posts Made By: JackMetal
Forum: Bioinformatics 01-11-2015, 08:19 PM
Replies: 1
Views: 2,703
Posted By JackMetal
Have you addressed this problem yet? I am having...

Have you addressed this problem yet? I am having the same issue.
Forum: Bioinformatics 09-30-2013, 02:54 PM
Replies: 11
Views: 4,378
Posted By JackMetal
Thanks. But when I run the script, it seems that...

Thanks. But when I run the script, it seems that I dont have all these modules, Bio, multiprocessing, os, sys etc. Does it mean I need to install all these modules listed to run the script.
Forum: Bioinformatics 09-28-2013, 10:30 AM
Replies: 11
Views: 4,378
Posted By JackMetal
Thank you so much. Can you give some direction on...

Thank you so much. Can you give some direction on how to wrap signalp with the script you provided?
Forum: Bioinformatics 09-28-2013, 09:24 AM
Replies: 11
Views: 4,378
Posted By JackMetal
The version I'm using is signalp-4.1. I'm reading...

The version I'm using is signalp-4.1. I'm reading your paper. It looks awesome. I might have some further questions about the Galaxy.
Forum: Bioinformatics 09-27-2013, 03:07 PM
Replies: 11
Views: 4,378
Posted By JackMetal
How to increase sequence limit in SignalP

I'm using SignalP in my local computer. One thing that I've encountered is 'Sequence limit reached: Max 10000 sequences are allowed'. I've read through the instructions, and did not find the command...
Forum: RNA Sequencing 09-25-2013, 07:47 AM
Replies: 4
Views: 5,462
Posted By JackMetal
Yes, you're right. It is more robust to use...

Yes, you're right. It is more robust to use entire assembly, since the result would be normalized by the entire mRNA expression, and also much easier for downstream analysis.
Forum: RNA Sequencing 09-24-2013, 09:25 AM
Replies: 4
Views: 5,462
Posted By JackMetal
I used RNA-seq analysis in CLC genomic workbench....

I used RNA-seq analysis in CLC genomic workbench.
Set parameters is as below
Minimum length fraction: 0.9
Minimum similarity fraction: 0.8
Maximum number of hits for a read: 10
What is the...
Forum: RNA Sequencing 09-24-2013, 08:23 AM
Replies: 4
Views: 5,462
Posted By JackMetal
Can I use a small subset of transcripts as a reference for RNA-seq analysis

Instead of using all the transcripts as reference for the RNA-seq analysis, can I use a small subset which I am interested? I compared the results, of course, the expression values from the small...
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