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
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
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