Hi everyone! I am an undergrad and pretty new in ChIP-seq. And I need to use bowtie with hg19. I indexed hg19 with bowtie-build and completed it. I would like to run my single-end fastq files with bowtie. I am using this to run bowtie.
bowtie --large-index </home/cilga/Desktop/VPC/ref/bowtie_indexes/bt1/hg19> -q /home/cilga/Desktop/VPC/chipseq/samples/dht_treatment/SRR3728821_pass.fastq -S SRR3728821.sam
I am not sure whether I do wrong. And I got this error:
Could not locate a Bowtie index corresponding to basename "/home/cilga/Desktop/VPC/chipseq/samples/dht_treatment/SRR3728821_pass.fastq" Command: bowtie --wrapper basic-0 -S /home/cilga/Desktop/VPC/chipseq/samples/dht_treatment/SRR3728821_pass.fastq SRR3728821.sam
Is there anyone can help me? Thank you for your helps.
PS.. can someone write an example command for bowtie?