SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 10 of 10
Search took 0.00 seconds.
Search: Posts Made By: luxmare
Forum: RNA Sequencing 06-26-2011, 05:25 PM
Replies: 4
Views: 6,046
Posted By luxmare
Hi Ickou, As you may already know, The...

Hi Ickou,

As you may already know, The recommended parameters for very short reads were described in the release note of TopHat 1.3.1 as below.



Hope this helps.

Thank you,
Forum: Bioinformatics 01-12-2011, 03:37 PM
Replies: 6
Views: 5,640
Posted By luxmare
To remove erroneous lines from TopHat SAM file, I...

To remove erroneous lines from TopHat SAM file, I wrote a perl script by myself. But it's not quick tool. I also want to have a quick tool for that.



Also in our system, the latest version of...
Forum: Bioinformatics 01-11-2011, 09:15 PM
Replies: 6
Views: 5,640
Posted By luxmare
Hi jb2, Sometimes, I also faced to the same...

Hi jb2,

Sometimes, I also faced to the same problem. The latest version of TopHat often report erroneous read alignments. The problem in sam to bam file conversion seems to be caused by the...
Forum: General 12-20-2010, 04:18 PM
Replies: 4
Views: 4,889
Posted By luxmare
Thank you fkrueger. I really think so, it's...

Thank you fkrueger.
I really think so, it's weird. I hope this hidden bias will be improved in the near future.
Forum: General 12-17-2010, 08:34 PM
Replies: 4
Views: 4,889
Posted By luxmare
Thank you, kmcarr. Do you mean that such weird...

Thank you, kmcarr.
Do you mean that such weird distribution is caused by the base calling algorithm in the illumina pipeline?

Can we just ignore the length distribution after trimming of...
Forum: General 12-15-2010, 08:50 PM
Replies: 4
Views: 4,889
Posted By luxmare
Question Periodical illumina read length distribution after trimming of low-quality bases

In my NGS data analysis, before mapping, I trimmed low-quality bases (<Q20) from 3' ends until a high quality (≥Q20) base appears. After that, I plotted the distribution of read length and obtained...
Forum: Bioinformatics 07-21-2010, 09:25 PM
Replies: 2
Views: 2,643
Posted By luxmare
The gaps means uncovered genomic positions. The...

The gaps means uncovered genomic positions. The sites without reads are not reported.
Forum: Bioinformatics 06-13-2010, 04:20 PM
Replies: 3
Views: 4,005
Posted By luxmare
Unhappy Hi Torst, Thank you for your reply. I agree...

Hi Torst,
Thank you for your reply. I agree with you. Quality scores of deletions is informative. But if the pileup format (made by BWA->SAMtools) was designed based on the IDEA you said, inserted...
Forum: Bioinformatics 06-08-2010, 06:50 PM
Replies: 3
Views: 4,005
Posted By luxmare
Unhappy deletion '*' has quality score in pileup?

I know that asterisks '*' in read bases column represent deletions as place holders in pileup format. But in my data, deletion '*' seems to has base quality score. why deleted bases have base...
Forum: Bioinformatics 06-03-2010, 07:25 PM
Replies: 1
Views: 2,795
Posted By luxmare
Unhappy Cufflinks on Solaris (compile error)

I want to install Cufflinks (the latest version 0.8.2) on Solaris 10 server.

I've already installed Boost C++ libraries Version 1.43.0 on the system. But I faced to the following errors when I...
Showing results 1 to 10 of 10

 


All times are GMT -8. The time now is 05:58 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO