Seed length doesnt match number of aligned reads in SAM file
Hi,
I ran the bowtie2 on a set of fastq reads whose linker sequence have been trimmed. After alignment, I obtained the SAM file. When I opened it, I found there are several alignments less than 20 nucleotides.
When by default the seed length of bowtie2 in "end-to-end_alignment" is 22, how can I end up finding some reads which has less than 20 nucleotides aligned? The code for bowtie2 is given as follows:
bowtie2 -p 30 -x /bowtie2_indexes/ref -U Sample_1_only_rRNA.fastq -S Sample_1.sam
Kindly guide me.
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Presumably it changes the seed size in such cases. This isn't documented anywhere, you'll have to go through the bowtie2 source code to find out exactly what's going on.
Hi Devon Ryan,
Thanks for your suggestion, I will try to look into
bt2_search.cppfile, Hope I find the reason. I am working with ribosomal profiling where the size of reads are between 27 - 32 nucleotides. Does this has anything to do with alignment?You'll need to look in the C++ code, not the perl wrapper. I'm not going to look for this for you, you'll have to look yourself if you really want to know.