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Search: Posts Made By: yingzhang
Forum: Bioinformatics 05-24-2013, 10:28 AM
Replies: 19
Views: 19,484
Posted By yingzhang
For Tophat/1.0 + version, tophat outputed a MAPQ...

For Tophat/1.0 + version, tophat outputed a MAPQ value of 255 to indicate the mapping is unique or not. So for bam file, you can ran "samtools view -q 255" to extract all uniquely mapped reads.
...
Forum: Bioinformatics 04-04-2013, 08:53 AM
Replies: 2
Views: 3,390
Posted By yingzhang
If you are not trying to submit a PBS job for...

If you are not trying to submit a PBS job for megan, you can try the following commands:

./MEGAN +g false -x <commands>

Here is my terminal:

$ MEGAN +g false -x "import...
Forum: Bioinformatics 11-27-2012, 11:24 AM
Replies: 1
Views: 2,200
Posted By yingzhang
I think tophat-fusion-post is written in python. ...

I think tophat-fusion-post is written in python.

Here is my answers to part of your questions.

1. Symbolic link. Yes, I used symbolic links for blast database.
2. Since it is symbolic link, I...
Forum: Bioinformatics 11-26-2012, 11:43 AM
Replies: 40
Views: 18,127
Posted By yingzhang
extreme memory requirement for Tophat-fusion-post

After 3 failed tophat-fusion-post runs on the sample MCF data, I finally got the program to work.

This is the setting of my successful job:

#PBS -l mem=64gb,nodes=1:ppn=8,walltime=24:00:00
...
Forum: RNA Sequencing 05-18-2012, 12:34 PM
Replies: 6
Views: 4,361
Posted By yingzhang
I will first check whether the gtf file is in the...

I will first check whether the gtf file is in the right format. Then I will check whether I have allocated enough memory for TopHat. My job once got killed at the exact step because it used much...
Forum: Bioinformatics 05-18-2012, 09:21 AM
Replies: 8
Views: 10,737
Posted By yingzhang
I don't think your GTF file is in the right...

I don't think your GTF file is in the right format.

According to UCSC, GTF file contains 9 column:
<seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes]
Forum: RNA Sequencing 05-04-2012, 08:25 AM
Replies: 2
Views: 1,720
Posted By yingzhang
If you have ever run samtools flagstat on Tophat...

If you have ever run samtools flagstat on Tophat output (accepted_hits.bam), you will always see a fairly low percentage of mapped reads properly paired. This is NOT because Tophat can't pair reads,...
Forum: RNA Sequencing 05-01-2012, 10:49 AM
Replies: 9
Views: 4,788
Posted By yingzhang
I didn't use the option "--fusion-search". Based...

I didn't use the option "--fusion-search". Based on the manual, I think the option is turned off by default.
Forum: RNA Sequencing 05-01-2012, 10:40 AM
Replies: 9
Views: 4,788
Posted By yingzhang
A slightly different memory issue

I am test driving TopHat 2.0 on a linux cluster.

I prepared 4 sample sets, which contain 13 million to 18 million 50bp paired reads. Tophat was called to process them one by one. I initialized...
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