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Hi ians,
I think Trinity do accept Paired End Reads as separate files. Please refer to Trinity Manual for more information.
http://trinityrnaseq.sourceforge.net/Leave a comment:
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ians, imo 'no paired read' mode means the same you infer to me as well = no insert size info.Leave a comment:
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If it said so in the read-me....
However Butterfly should use read pairs. You might want to download the whole Trinity package and read the manuscript
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inchworm and paired ends
I recently read in the installation README that:
"There is no 'paired read' mode currently in inchworm. It treats each read independently. If you have pairs, just include them all in a single fasta file with the sequences properly oriented for strand-specificity (sense strand)."
Does this mean that inchworm does not take insert size information inconsideration when assembling scaffolds?
Does Butterfly use insert size info to assemble scaffolds?Last edited by ians; 10-04-2011, 02:44 PM.
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