Hii everyone i have read about conversion of Fastq to sam through picard tools and alignment with bowtie(which directly gives sam output) both dnt worked out with my fastq files ? please suggest any other way? thanks in advance
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Hii dpryan
Thanks i could successfully install and run bowtie2 to some extend. but after creating the reference index file and when i was trying to align reads it is showing an error like
Extra parameter(s) specified: "reads1.fq", "lambda.sam"
Error: Encountered internal Bowtie 2 exception (#1)
bowtie2-align exited with value 1
any one please suggest how to sort this.
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