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Old 03-20-2011, 10:41 PM   #5
Junior Member
Location: washington area

Join Date: Mar 2011
Posts: 7
Default elsewhere documented errors with samtools

Hi Jon,

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

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

Both are excellent articles....

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