trimmed length used; newbler

[anna_]

Hi,

in the newbler output file 454 trimStatus there are raw lenght, trimmed length and trimmed length used for each read.

Is this right:

raw lenght: length before image processing
trimmed length: length after trimming be the "image"-software of the GS FLX
trimmed lenght used: length after trimming by newbler or (in other words) newbler input for assembly

???

To which of these read lengths do the statistics in the newblerMetrics file refer?

Thanks, anna.

[RCJK]

Maybe this helps:

http://contig.wordpress.com/2010/05/20/newbler-output-vi-the-%E2%80%98status%E2%80%99-files-454trimstatus-txt-454readstatus-txt-454pairstatus-txt-and-the-454alignmentinfo-tsv-file/#more-108

[anna_]

Thanks RCJK,

but I know this link already. It says: Used Trimmed Length: the length of the part of the read newbler used.

So that means that theses lenght are the input for the assembly. So now the question:

Is the number of bases that is given at the beginning of the Metrics file the number of bases that was used as the assembling input OR the number of bases that came out of the GS FLX?

(Maybe this is very clear for people who are used to see data like this, but I have never seen newbler output before)

[vamosia]

As far as I know, prior to assembly, newbler will trim the reads back using its own set of separate parameter. So the trimmed reads (by newbler) are used as the input for the algorithm.

So in theory the statistics in the NewblerMetrics should be derived from these numbers (trimmed lenght used), since these were the input reads.