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Search: Posts Made By: john_mu
Forum: Bioinformatics 10-22-2010, 10:27 AM
Replies: 13
Views: 5,831
Posted By john_mu
Hi marcowanger, The cufflinks compatible...

Hi marcowanger,

The cufflinks compatible file doesn't include the clipped part of the alignments. Since some alignments might be not be able to find the other end of the split read, we still keep...
Forum: Bioinformatics 10-21-2010, 12:34 PM
Replies: 13
Views: 5,831
Posted By john_mu
Ah I see, sorry I had not played with the new...

Ah I see, sorry I had not played with the new version much yet. You are probably right.
Forum: Bioinformatics 10-20-2010, 10:23 AM
Replies: 13
Views: 5,831
Posted By john_mu
This is a shameless plug. But as far as I know...

This is a shameless plug. But as far as I know TopHat does not yet support that.
SpliceMap is able to deal with such kind of reads natively.
Forum: Bioinformatics 10-10-2010, 05:01 PM
Replies: 1
Views: 1,205
Posted By john_mu
This greatly depends on the type of data you wish...

This greatly depends on the type of data you wish to map. In my opinion, with the current types of short reads there is not much speed up to be gained from using GPGPU. Hence, as far as I know nobody...
Forum: Bioinformatics 09-21-2010, 09:11 AM
Replies: 2
Views: 2,738
Posted By john_mu
Yes the nucleotide distribution is useful. ...

Yes the nucleotide distribution is useful.

If the distribution seems "uneven" at the beginning, that could indicate some residual adaptor sequences. The unevenness should be obvious when you...
Forum: Bioinformatics 09-21-2010, 09:08 AM
Replies: 1
Views: 1,392
Posted By john_mu
If you use the sort command suggested by...

If you use the sort command suggested by cufflinks

Something like this (it should be printed out when it gives the sorting error):
sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted

Then it will...
Forum: RNA Sequencing 09-16-2010, 02:49 PM
Replies: 2
Views: 2,773
Posted By john_mu
Hi, The strand info will only be on the...

Hi,

The strand info will only be on the junction reads. It is impossible to determine the strand of non-junction hits without using a stranded protocol in the experiment.

column 2 is the SAM...
Forum: Bioinformatics 09-07-2010, 02:34 PM
Replies: 0
Views: 2,544
Posted By john_mu
SpliceMap 3.3.3.x released: Tool for spliced read alignment

Hi Everyone,

SpliceMap 3.3.3.x has been release with many user requested features and stability/reliability enhancements.

Website: http://www.stanford.edu/group/wonglab/SpliceMap/

The...
Forum: Bioinformatics 09-04-2010, 01:13 PM
Replies: 2
Views: 2,187
Posted By john_mu
using "seq_*.fa" won't work with bowtie-build,...

using "seq_*.fa" won't work with bowtie-build, the output won't be all your sequence files.

If you want to input a list you need to separate each file with commas.

I'm not sure why it fails...
Forum: Bioinformatics 09-03-2010, 12:46 PM
Replies: 8
Views: 1,911
Posted By john_mu
Yes I noticed that, they are quite odd... I just...

Yes I noticed that, they are quite odd... I just replace them with N's when doing analysis.
Forum: Bioinformatics 08-27-2010, 10:17 AM
Replies: 8
Views: 3,636
Posted By john_mu
There is a new program called HMMsplicer that was...

There is a new program called HMMsplicer that was designed for the Arabidopsis genome. Maybe you can give that a try.

I haven't personally used it, but they were benchmarking it against SpilceMap...
Forum: Bioinformatics 08-25-2010, 01:07 PM
Replies: 16
Views: 7,008
Posted By john_mu
Yes, more memory. Sequencers are only going to...

Yes, more memory. Sequencers are only going to spit out more reads.

Also, more memory usually means programs can potentially run faster.
Forum: Bioinformatics 08-25-2010, 12:22 PM
Replies: 19
Views: 8,199
Posted By john_mu
I hope that works. I'm trying to think why...

I hope that works.

I'm trying to think why that might be the case.. If it still doesn't work
could you email me the log files as described in
...
Forum: Bioinformatics 08-25-2010, 11:49 AM
Replies: 19
Views: 8,199
Posted By john_mu
Hi, Does the example data set in the...

Hi,

Does the example data set in the tutorial work?
Forum: Bioinformatics 08-24-2010, 10:30 AM
Replies: 3
Views: 1,689
Posted By john_mu
I'm guessing it is not ready for a general...

I'm guessing it is not ready for a general audience yet.

You could try to email the Author

http://www-personal.umich.edu/~kning/
Forum: Bioinformatics 08-24-2010, 10:26 AM
Replies: 11
Views: 4,323
Posted By john_mu
http://biogibbs.stanford.edu/~jiangh/SeqMap/ ...

http://biogibbs.stanford.edu/~jiangh/SeqMap/

SeqMap allows up to 5 mismatches/deletions

But it is slower than the other aligners if you want to take advantage of this feature.
Forum: Bioinformatics 08-23-2010, 11:42 AM
Replies: 4
Views: 3,149
Posted By john_mu
SpliceMap does separate multi-reads, you could...

SpliceMap does separate multi-reads, you could check the paper to see if it suits your purpose. Although the paper does describe an older version, it gives the main idea.

The link is in my...
Forum: Bioinformatics 08-23-2010, 11:40 AM
Replies: 15
Views: 16,774
Posted By john_mu
Did you check if the reads are forward-reverse?...

Did you check if the reads are forward-reverse? or some other orientation?
Forum: Bioinformatics 08-19-2010, 12:20 PM
Replies: 5
Views: 2,255
Posted By john_mu
EDIT: has been answered

EDIT: has been answered
Forum: Bioinformatics 08-18-2010, 06:24 PM
Replies: 14
Views: 3,635
Posted By john_mu
You should convert the SAM file to a BAM file for...

You should convert the SAM file to a BAM file for input into IGV.

It does require a lot of memory if you have a large number of reads. That could be why it is freezing.
Forum: Bioinformatics 08-18-2010, 11:05 AM
Replies: 14
Views: 3,635
Posted By john_mu
I may help to also display the SAM file in IGV so...

I may help to also display the SAM file in IGV so you can see where the reads are aligning.
Forum: Bioinformatics 08-12-2010, 10:42 AM
Replies: 19
Views: 8,199
Posted By john_mu
hmm... are you saying that you get output in the...

hmm... are you saying that you get output in the coverage and SAM file but no junctions? That is extremely odd....

Could you email me your terminal output? johnmu (at) stanford (dot) edu

I'll...
Forum: Bioinformatics 08-08-2010, 09:51 AM
Replies: 3
Views: 3,565
Posted By john_mu
If I remember correctly, it outputs the other...

If I remember correctly, it outputs the other ones in the "XA" tag at the end of the line.

if you set the -n option to a high number, you should get most of the hits.

I think the hits are...
Forum: Bioinformatics 08-07-2010, 09:49 PM
Replies: 3
Views: 3,565
Posted By john_mu
I thought it did this by default? from the...

I thought it did this by default?

from the manual:

By default, if the best hit is no so repetitive (controlled by -R), BWA also finds all hits contains one more mismatch; otherwise, BWA finds...
Forum: Bioinformatics 08-05-2010, 10:59 AM
Replies: 12
Views: 3,673
Posted By john_mu
I'm not sure what could be wrong. Could you...

I'm not sure what could be wrong.

Could you send me your output from the command line and your "run.cfg" and i'll take a look.

Also, which version of SpliceMap are you using?

You can email...
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