Question: metatranscriptomic read mapping
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gravatar for bsp017
2.2 years ago by
bsp01720
Wales, Bangor, Bangor Uni
bsp01720 wrote:

I mapped a depleted metatranscriptome bam file against a reference bacterial genome. Some genes have a 'substantial' number of reads mapping. I have previously isolated this bacteria from the sequencing site. Is there a method where I could say that x number of genes from this bacteria are expressed, therefore this bacteria is functionally active within the microbiome?

I have looked at the mapping data in Artemis and some genes are expressed >1000 times. How may reads constitute evidence of expression in a metatranscriptome? 

Thanks

 

rna-seq alignment • 1.0k views
ADD COMMENTlink modified 2.1 years ago by Brian Bushnell14k • written 2.2 years ago by bsp01720

Whether something is significant also depends on the denominator (total number of mapped reads).  If you map 2 trillion Illumina reads, and generate conclusions based on a study that used 2000 Sanger reads, using the same absolute cutoffs, your results will be wrong.

Even ignoring that...  I think it's much more important to do things because they make sense in the context of your experiment, than because some random unrelated paper happened to do that thing and got through the review process.  I consider that to be bad science.

ADD REPLYlink written 2.1 years ago by Brian Bushnell14k
0
gravatar for bsp017
2.1 years ago by
bsp01720
Wales, Bangor, Bangor Uni
bsp01720 wrote:

In response to my question, I found this paper; http://t.co/snb0U82HVZ which maps metatranscriptome files against an antibiotic resistance gene database. If reads map more than 3 times to a gene and span > 200 bp of that gene then it's considered significant.

 

ADD COMMENTlink written 2.1 years ago by bsp01720
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