[BioC] any package to do gene expression value estimation

[Wei Shi]

Hi Shan Gao,

Neither BWA or Bowtie can map junction reads which span two or more exons. You may try the Subread aligner implemented in Rsubread package which can map junction reads in addition to exonic reads. The percentage of junction reads in an RNA-seq dataset is typically around 20%. So you should be able to map ~20% more reads using Subread compared to Bwa or Bowtie.

The Rsubread package also includes a function called featureCounts which counts the number of reads falling into each gene or each exon and returns you a list object which contains a table of read counts and also annotation information.

If your worry about the efficiency, this might be the package for you. Rsubread is at least twice as fast as bowtie (and a lot faster than Bwa). The featureCounts() function only takes ~2 minutes to summarize mapping information from a SAM format file into a table of read counts.

Cheers,
Wei

On Oct 26, 2011, at 1:05 AM, wang peter wrote:

>> 
>> dear Martin:
>>         your answer is quite clear. i will try  Biostrings::matchPDict to
>> map the reads of each sample to the assembled transcriptome using those
>> samples.
>> 
>>         but what i worrry is the efficiency. i can also use BWA OR bowtie
>> to do so.
>> 
>> i donot know if Biostrings::matchPDict  will be very slow?
>> 
>> thank you
>> 
>> shan gao
>> 
> 
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