After what Devon say about trimming
What I am using
$BT2_HOME/bowtie2 --local -x specious -U $BT2_HOME/example/reads/longreads.fq -S eg.sam
-U Comma-separated list of files containing unpaired reads to be aligned, e.g.
lane1.fq,lane2.fq,lane3.fq,lane4.fq. Reads may be a mix of different lengths. If
- is specified,
bowtie2 gets the reads from the "standard in" or "stdin" filehandle.
-x The basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final
.rev.1.bt2 / etc.
bowtie2 looks for the specified index first in the current directory, then in the directory specified in the
BOWTIE2_INDEXES environment variable.
-S File to write SAM alignments to. By default, alignments are written to the "standard out" or "stdout" filehandle (i.e. the console).
If your data not indexed use
$BT2_HOME/bowtie2-build -f ~/path/to/your/genome.fa ~/where/you want/index/to/be/nameOfTheIndex
summary of the parameters: http://chipster.csc.fi/manual/bowtie2-paired-end.html
for more visit http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
Thank you Devon Ryan for reply. i want to ask you one more thing that, right now i am not focusing on the sequence assembly. just mapping reads to find SNPs, so local mode is more appropriate ?
My reply neither mentioned nor had even the remotest thing to do with sequence assembly, so I'm not sure why you're even mentioning it. As I mentioned in my reply, using local alignment will often give a bit better results, since end-to-end alignment won't work well when variants occur at the end of reads (whereas local alignment will just soft-clip these sequences).
okay. Thanks i got your point !!