Hello Jianguang, In simple terms, "No" produces a strict alignment and "Yes" produces a more permissive alignment. The option 'Allow indel search:' is a way of allowing for variability in your data (presumably biologically valid) to not be interpreted as mismatches or gaps. Mismatches/gaps in an alignment lower the overall score and can lead to alignment failures. The default for this parameter is "Yes" with value of 3 for insert/deletion length in Galaxy (allowing for simple nucleotide polymorphism variability up to a single codon, per position, in either the query or target). All values can be modified. If this interferes with your data mapping accurately, then it could be disabled by setting the parameter to "No". A test comparing the two alternatives on a sample would be a good way to see how this single change affects your particular sample. Good questions to ask: What reads do not map when the stricter alignment rules are applied? Do any reads map with a change in specificity? Do you agree with the results? Hopefully this helps! Jen Galaxy team On 8/15/12 1:21 PM, Du, Jianguang wrote:

Dear All,

I want to compare the pre-mRNA alternaive splicing events between RNA-seq datasets. Do I need to allow indel search when I run Tophat? What is the indel search for? I could not find detail information about "indel search" through the documentation of Tophat.

Thanks.

Jianguang Du

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