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adeslat · 03-20-2011, 10:41 PM

Hi Jon,

I was looking at "Scripture" and found looking through their course material at:

http://molecularevolution.org/resour...pture_activity

the following:

"There is currently an incompatibility between samtools sort and Picard (which is used by Scripture); therefore you need to sort the BAM file using Picard and not samtools:"

By the way -- the instructions on this site are spot on, clean and complete.

The reference is the same Nature Biotechnology issue where the Steven Salzberg and Cole Trapnell so nicely introduced the "Tuxedo" suite in the letter "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation"
Cole Trapnell, Brian A Williams,Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold & Lior Pachter
Nature Biotechnology 28, 511–515 (2010) doi:10.1038/nbt.1621

Scripture is discussed in:
"Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs" - pp503 - 510
Mitchell Guttman, Manuel Garber, Joshua Z Levin, Julie Donaghey, James Robinson, Xian Adiconis, Lin Fan, Magdalena J Koziol, Andreas Gnirke, Chad Nusbaum, John L Rinn, Eric S Lander & Aviv Regev
doi:10.1038/nbt.1633

Both are excellent articles....

Anne

03-20-2011, 10:41 PM	#5
adeslat Junior Member Location: washington area Join Date: Mar 2011 Posts: 7	elsewhere documented errors with samtools Hi Jon, I was looking at "Scripture" and found looking through their course material at: http://molecularevolution.org/resour...pture_activity the following: "There is currently an incompatibility between samtools sort and Picard (which is used by Scripture); therefore you need to sort the BAM file using Picard and not samtools:" By the way -- the instructions on this site are spot on, clean and complete. The reference is the same Nature Biotechnology issue where the Steven Salzberg and Cole Trapnell so nicely introduced the "Tuxedo" suite in the letter "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation" Cole Trapnell, Brian A Williams,Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold & Lior Pachter Nature Biotechnology 28, 511–515 (2010) doi:10.1038/nbt.1621 Scripture is discussed in: "Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs" - pp503 - 510 Mitchell Guttman, Manuel Garber, Joshua Z Levin, Julie Donaghey, James Robinson, Xian Adiconis, Lin Fan, Magdalena J Koziol, Andreas Gnirke, Chad Nusbaum, John L Rinn, Eric S Lander & Aviv Regev doi:10.1038/nbt.1633 Both are excellent articles.... Anne