Bowtie error: Could not locate a Bowtie index corresponding to basename

Question

[cilgaiscan]

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?

[WouterDeCoster]

I believe the error message does not match with the command you pasted above. Can you check again that it is effectively the command you used?

[cilgaiscan]

yes i double checked. i use same command and got same error..

[WouterDeCoster]

The error says:

Command: bowtie --wrapper basic-0 -S /home/cilga/Desktop/VPC/chipseq/samples/dht_treatment/SRR3728821_pass.fastq SRR3728821.sam

Are you sure you didn't swap some arguments there?

[cilgaiscan]

i am.i used the arguments i shared in my question :(

[GenoMax]

cilgaiscan : You are not actually including <> around the large index file location in your command, correct?

Answer 1

[h.mon]

Try the following:

bowtie -S -q --large-index /home/cilga/Desktop/VPC/ref/bowtie_indexes/bt1/hg19 /home/cilga/Desktop/VPC/chipseq/samples/dht_treatment/SRR3728821_pass.fastq > SRR3728821.sam

The problem, I believe, is for bowtie -S is just a boolean flag, and you are using it as in bowtie2, where -S file.sam creates the output file, instead of using stdout.