TopHat - Bowtie read trimming

[adrian]

Hello:

I am using TopHat for aligning RNA-Seq reads and map exon junctions.

I am familiar with BWA and skimming through Bowtie (that tophat uses for alignment) and wondering if Bowtie has quality trimming option.

Something similar to BWA aln -q option. Here -q removes the 3' bases if the quality is below a threshold.

bwa aln -q 20 mysamp.fastq

my fasta reads 3' ends have very low quality bases.

thanks
Adrian

[kokonech]

Why not use an external filter? For example, here's a simple Biopython scirpt to filter reads that have quality below some fixed value.

[anamika]

Sangenix : Can perform Trimming of reads based upon Quality Score

Sangenix Qc and Trimming option , can remove the low quality filter , based upon user input in an auto mated way. Minimal user interference for execution of workflow and excellent result output

http://www.sangenix.com/