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Old 07-26-2012, 01:10 AM   #1
Location: Italy

Join Date: Jul 2010
Posts: 27
Default Mask x number of bases WITHIN sequence prior to alignment

Hi all,

As you may see from the picture I have this QC from all R2 reads of my Paired End sequenced samples. Due to a technical error during the sequencing I am ending up with 30+ R2 reads with serious errors in the middle of the sequence.

Do you know any way to mask (or to allow mismatch at) a specific number of bases (2-3) at a specific position WITHIN the fragment length prior to alignment? Biostrings is an option that I would prefer not to use for reasons of speed.

Can what you propose applied selectively to only one of the two reads in the paired end samples?

It would be ideal if this could be directly applied directly with Bowtie like the trimming left/right that already exists as an inherent option.

Last edited by SEQond; 07-26-2012 at 04:51 AM. Reason: Amelioration of description
SEQond is offline   Reply With Quote

alignment, mask, mismatch, within sequence

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