I've been using the latest version of Bowtie2 to map 100 base Illumina reads for RNA-seq. I am also trimming 25 bases from the 3' end.
I've mapped this sort of data before with TopHat and haven't come across problems. However, I don't understand certain aspects of the .sam output that Bowtie2 gives me:
1. The output contains ALL reads, whether mapped or not - not too much of a problem since I can filter out the unmapped reads anyway
2. In some cases, the base quality scores are non-existent (just represented by "*"). I've checked the .fastq files that I supplied to Bowtie2, and these do contain the base quality scores for these reads. I thought at first that it was only missing on unmapped reads, but it is also missing on reads that have mapped.
Any help would be greatly appreciated.
I've mapped this sort of data before with TopHat and haven't come across problems. However, I don't understand certain aspects of the .sam output that Bowtie2 gives me:
1. The output contains ALL reads, whether mapped or not - not too much of a problem since I can filter out the unmapped reads anyway
2. In some cases, the base quality scores are non-existent (just represented by "*"). I've checked the .fastq files that I supplied to Bowtie2, and these do contain the base quality scores for these reads. I thought at first that it was only missing on unmapped reads, but it is also missing on reads that have mapped.
Any help would be greatly appreciated.
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