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Search: Posts Made By: xuguorong
Forum: Pacific Biosciences 03-07-2017, 09:14 PM
Replies: 4
Views: 1,988
Posted By xuguorong
Thank you so much! Canu looks cool and I will try...

Thank you so much! Canu looks cool and I will try it!
Forum: Pacific Biosciences 03-07-2017, 09:07 PM
Replies: 4
Views: 1,988
Posted By xuguorong
Thank you so much! I will try FALCON!

Thank you so much! I will try FALCON!
Forum: Pacific Biosciences 03-03-2017, 02:44 PM
Replies: 4
Views: 1,988
Posted By xuguorong
Can SMRT analysis pipeline support fastq files?

Hello,

I am new to PacBio data and pipeline. Recently, I got some pacBio data in fastq format instead of bas.h5 format. I tried blasr to run alignment and looks like blasr worked. But I want to...
Forum: Bioinformatics 06-27-2016, 09:04 AM
Replies: 136
Views: 38,300
Posted By xuguorong
Hi Felix, Thank you so much for your new...

Hi Felix,

Thank you so much for your new release!
The new features definitely can remove all Ns from the reads! Awesome!

For the question 1, I want to try run cutadapt three times to keep the...
Forum: Bioinformatics 06-24-2016, 10:57 AM
Replies: 136
Views: 38,300
Posted By xuguorong
Hi Felix, Thank you so much for your...

Hi Felix,

Thank you so much for your response!

For the question 1:
After trimming, the length of the left sequence is only 7nt but the length of the right sequence is 21nt. Obviously I want...
Forum: Bioinformatics 06-24-2016, 10:05 AM
Replies: 136
Views: 38,300
Posted By xuguorong
Recently I am using your tool Trim Galore to trim...

Recently I am using your tool Trim Galore to trim the adapter string from our miRNA sequencing data. It is amazing tool and very fast! Thanks a lot for your great job! When I looked into the...
Forum: Bioinformatics 11-09-2012, 08:17 AM
Replies: 3
Views: 1,385
Posted By xuguorong
Thank you so much, dpryan! I fixed this issue...

Thank you so much, dpryan!
I fixed this issue after improving the unique mapping rate!
Forum: Bioinformatics 11-07-2012, 05:56 PM
Replies: 3
Views: 1,385
Posted By xuguorong
Nobody knows how to run HTSeq with paired-end...

Nobody knows how to run HTSeq with paired-end reads?
Forum: Bioinformatics 10-26-2012, 12:28 PM
Replies: 3
Views: 1,385
Posted By xuguorong
How to run HTSeq with paired end file

I have one paired end SAM file generated by Novoalign. The two ends of one pair share the same read ID, but the HTSeq reports all of them as "alignment_not_unique" and ignores them. Anybody know how...
Forum: Bioinformatics 10-23-2012, 07:08 PM
Replies: 8
Views: 10,518
Posted By xuguorong
Hi Simon, I am very wondering the paired-end...

Hi Simon,

I am very wondering the paired-end sorting problem before using HTSeq.
I read many posts about this issue, but no standard and complete thread explain it.
At first, I sort my...
Forum: Bioinformatics 08-14-2012, 01:20 PM
Replies: 0
Views: 777
Posted By xuguorong
how to suppress the error messages from cuffdiff?

Recently, I am trying to run cuffdiff by importing the SAM files generated by Novoalign. I got many error messages on the console as the following,
BAM record error: found spliced alignment without...
Forum: Bioinformatics 03-14-2012, 07:28 PM
Replies: 0
Views: 1,115
Posted By xuguorong
RNA CoMPASS v1.0 released!

RNA CoMPASS, a web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis...
Forum: Bioinformatics 05-02-2011, 11:29 AM
Replies: 4
Views: 4,398
Posted By xuguorong
Hi RDW, Thank you for your reply! Yes, I...

Hi RDW,

Thank you for your reply!
Yes, I tried 32bit binary and it cannot process large files. I also tried to compile 64 bit from source code but failed. So I have to switch to Linux or Mac OS...
Forum: Bioinformatics 05-01-2011, 07:36 PM
Replies: 4
Views: 4,398
Posted By xuguorong
Hi RDW, I downloaded the 32bit binary bowtie...

Hi RDW,

I downloaded the 32bit binary bowtie from the sourceforge and tried to run on my 32bit Win 7 machine. The fasta/fastq file cannot exceed 10K reads, otherwise bowtie always exit...
Forum: Bioinformatics 04-27-2011, 02:23 PM
Replies: 4
Views: 4,398
Posted By xuguorong
Bowtie for Windows 7

I tried to install bowtie on my windows 7 32bit and 64bit, and I found it cannot align large size data set. When I used the indexes file of H. sapiens (2.7GB), bowtie told me that cannot load the...
Forum: Bioinformatics 04-21-2011, 11:46 AM
Replies: 3
Views: 1,385
Posted By xuguorong
Hi tonge, The current functionalities are...

Hi tonge,

The current functionalities are focused on mRNA isoform quantification and microRNA quantification would be released soon.

Thank you for using SAMMate!
Guorong
Forum: Bioinformatics 04-08-2011, 01:59 PM
Replies: 0
Views: 1,477
Posted By xuguorong
SAMMate 2.5 - Transcriptome quantification at the isoform-level using RNA-seq

All-new SAMMate 2.5 is released.

http://sammate.sourceforge.net/

New features:
RAEM-Read Assignment via EM (Deng et al. 2011, Nucleic Acids Research, doi: 10.1093/nar/gkr042)
One-step iQuant...
Forum: Bioinformatics 04-08-2011, 10:52 AM
Replies: 3
Views: 1,385
Posted By xuguorong
SAMMate 2.5 - Transcriptome quantification at the isoform-level using RNA-seq

All-new SAMMate 2.5 is released.

http://sammate.sourceforge.net/

New features:
RAEM-Read Assignment via EM (Deng et al. 2011, Nucleic Acids Research, doi: 10.1093/nar/gkr042)
One-step iQuant...
Forum: Bioinformatics 03-31-2011, 11:41 AM
Replies: 3
Views: 1,130
Posted By xuguorong
Hi, Thank you for using SAMMate! Quality...

Hi,
Thank you for using SAMMate!
Quality field is not important for SAMMate.
For pinpoint your sam file problem, could you post some reads for me?
Than I can check what's going on.

Thanks...
Forum: Bioinformatics 11-29-2010, 06:16 PM
Replies: 3
Views: 1,130
Posted By xuguorong
SAMMate 2.4.1 (Stable version) release

We have released SAMMate 2.4.1!
In this version, we have fixed some bugs including the bug that SAMMate 2.4 can not run on Windows XP.
The latest version can be downloaded from: ...
Forum: Bioinformatics 11-19-2010, 09:49 AM
Replies: 7
Views: 2,164
Posted By xuguorong
Hi Jack, I am sorry for late response! ...

Hi Jack,

I am sorry for late response!

We have released SAMMate 2.4.1 and we have fixed some bugs including the WinXP problem. Now, you can download SAMMate for WinXP from ...
Forum: Bioinformatics 09-17-2010, 08:52 AM
Replies: 7
Views: 2,164
Posted By xuguorong
Hi Balat and Bioinfo, I am sorry for this...

Hi Balat and Bioinfo,

I am sorry for this bug on Win XP machine!
We met this kind of problem on Win XP machine before and it was caused by some .dll files missing on Win XP OS. But these .dll...
Forum: Bioinformatics 09-14-2010, 08:14 AM
Replies: 7
Views: 2,164
Posted By xuguorong
Thank you for using SAMMate! We are planning...

Thank you for using SAMMate!

We are planning to make the software available to Linux users, but the release date has not been decided yet. Once the Linux version is ready, I will let you know.
Forum: Bioinformatics 09-11-2010, 05:04 AM
Replies: 7
Views: 2,164
Posted By xuguorong
SAMMate 2.4 release

Recently, we released SAMMate 2.4 on Sourceforge.net.
We added some new features and made many enhancements.
You can download it from the below link:
http://sammate.sourceforge.net

New...
Forum: Bioinformatics 05-10-2010, 09:48 AM
Replies: 3
Views: 1,847
Posted By xuguorong
Hi Mike, You can access the home page of...

Hi Mike,

You can access the home page of SAMMate to get the documentation and usage!

http://SAMMate.sourceforge.net

If you need any other help, please let me know!
Showing results 1 to 25 of 27

 


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