Re: help for RNA-Seq
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Nathan Salomonis
Apr 10, 2012, 12:50:07 PM4/10/12
to 王磊, alt_pre...@googlegroups.com
Greetings,
Although you can analyze a set of junction.bed files from TopHat by themselves in AltAnalyze, it works best if you can also build exon.bed files to include with these that provide counts for discrete exon regions in addition to junctions. The steps to do this are outlined here:
http://code.google.com/p/altanalyze/wiki/BAMtoBED
Basically, what you are doing is first telling AltAnalyze to build a file that contains all known exon genomic coordinates in addition to novel exons based on the junction information in your junction.bed files. Next, AltAnalyze produces a bed file to use with Unix software BEDTools (must install). This is done on the machine with all of your TopHat produced BAM files. When you next run the bamToBed utility of BEDTools, as described in the above link, an exon.bed file will be produced for each BAM file. You must then make sure your exon and junction bed files can be recognized as corresponding to the same sample by naming them like this:
sample1__junction.bed
sample1__exon.bed
AltAnalyze will know that these are the same sample and analyze exons and junctions appropriately. Example files are here: http://code.google.com/p/altanalyze/wiki/RNASeq_sample_data
Let me know if you have problems with this and include the AltAnalyze.log file that is saved to your results directory if you have problems.
Best,
Nathan Salomonis
Although you can analyze a set of junction.bed files from TopHat by themselves in AltAnalyze, it works best if you can also build exon.bed files to include with these that provide counts for discrete exon regions in addition to junctions. The steps to do this are outlined here:
http://code.google.com/p/altanalyze/wiki/BAMtoBED
Basically, what you are doing is first telling AltAnalyze to build a file that contains all known exon genomic coordinates in addition to novel exons based on the junction information in your junction.bed files. Next, AltAnalyze produces a bed file to use with Unix software BEDTools (must install). This is done on the machine with all of your TopHat produced BAM files. When you next run the bamToBed utility of BEDTools, as described in the above link, an exon.bed file will be produced for each BAM file. You must then make sure your exon and junction bed files can be recognized as corresponding to the same sample by naming them like this:
sample1__junction.bed
sample1__exon.bed
AltAnalyze will know that these are the same sample and analyze exons and junctions appropriately. Example files are here: http://code.google.com/p/altanalyze/wiki/RNASeq_sample_data
Let me know if you have problems with this and include the AltAnalyze.log file that is saved to your results directory if you have problems.
Best,
Nathan Salomonis
On Mon, Apr 9, 2012 at 11:58 PM, 王磊 <wln...@126.com> wrote:
Hello,I am interested in AltAnalyze, But it is obscure for "Output known and novel exons from junction.bed files with AltAnalyze " . I use Tophat result junction.bed -> Build exon coordinate bed file to obtain BAM file exon counts. Can you give me some advice? Thank you!error:UnicodeEncodeError: 'ascii' codec can't encode characters in position 30-31: ordinal not in range(128)
Traceback (most recent call last):
File "AltAnalyze.py", line 6303, in <module>
File "AltAnalyze.py", line 4734, in AltAnalyzeSetup
File "UI.pyc", line 3426, in getUserParameters
File "UI.pyc", line 3466, in getAPTLocations
UnboundLocalError: local variable 'apt_location' referenced before assignment
Exception in Tkinter callback
Traceback (most recent call last):
File "Tkinter.pyc", line 1410, in __call__
File "UI.pyc", line 493, in filecallback
File "UI.pyc", line 954, in getPath
File "UI.pyc", line 1552, in exportDefaultFileLocations
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