Question: Bowtie error: Could not locate a Bowtie index corresponding to basename
0
gravatar for cilgaiscan
2.1 years ago by
cilgaiscan50
Turkey
cilgaiscan50 wrote:

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?

ADD COMMENTlink modified 2.1 years ago by h.mon31k • written 2.1 years ago by cilgaiscan50

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?

ADD REPLYlink written 2.1 years ago by WouterDeCoster44k

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

ADD REPLYlink written 2.1 years ago by cilgaiscan50

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?

ADD REPLYlink written 2.1 years ago by WouterDeCoster44k

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

ADD REPLYlink written 2.1 years ago by cilgaiscan50

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

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by genomax89k
0
gravatar for h.mon
2.1 years ago by
h.mon31k
Brazil
h.mon31k wrote:

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.

ADD COMMENTlink written 2.1 years ago by h.mon31k
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