Newbler Trim Status

[blindtiger454]

I have a combination of 454 and Illumina reads. I am interested in using programs such as velvet, mira, etc. I know that these programs require the reads be trimmed of polyA tails, vectors, bad quality, etc. The Newbler assembler program will automatically trim reads of polyA tails and bad quality, and the sequencing keys. This trim information is outputted in the 454TrimStatus.txt file. Instead of using programs such as Lucy or Seqclean for my 454 reads, can I just use the trim points from the TrimStatus file?

[flxlex]

Yes, you can. Even better, if you add the -tr option to newbler, it will output the trimmed reads in fasta format, with a corresponding qual file.

[BaCh]

I have a combination of 454 and Illumina reads. I am interested in using programs such as velvet, mira, etc. I know that these programs require the reads be trimmed of polyA tails, vectors, bad quality, etc.

I suspect we're talking about EST / RNASeq reads here, right?

If so: MIRA has own routines to clip sequences, and as with other assemblers, you should be very careful not to trim your data set twice! E.g.: the first time, a poly-A trim might indeed clip away the poly-A, but if you perform it a second time on the trimmed sequence, you might get unlucky and a comparatively long A-stretch within the valid sequence might then be mistaken as sequence to be clipped. Not good.

Anyway: either use a trimmed data-set and then tell all assemblers not to perform certain clippings, or take the original data set and tell the assemblers what to trim.

B.