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closeConfused as to the nature of the N. crassa sample?
Posted by David_Rinker on 11 Sep 2015 at 20:28 GMT
"N. crassa" is the obvious outlier in your analysis and is also the only species to not display polycistronic transcripts. The Methods section states that the data for "N. crassa" was from a separate study (Kim et al 2014), however, Kim et al was sequencing DNA (not RNA). Can you clarify as to why this gDNA-based sample was included in the present study and speculate as to why the analysis pipeline failed to note any reads mapping to intergenic regions. Thank you.
RE: Confused as to the nature of the N. crassa sample?
etseng replied to David_Rinker on 15 Sep 2015 at 22:17 GMT
Hi,
Both gDNA and cDNA was generated for the N. crassa dataset. However the authors were mainly only interested in the genome and thus the paper only included the genome portion.
This poster from the JGI user group meeting shows that cDNA was indeed generated for the same species:
https://s3.amazonaws.com/...
We are not certain why there were no polycistronic candidates. The sequencing depth on the sample was quite deep (the actual numbers escape me now, but I remember them being comparable to the P. crispa sample) so sequencing depth is not likely an argument.
Cheers,
Elizabeth Tseng (co-author)