Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Bowtie 2 error
0
gravatar for shambyross
22 months ago by
shambyross • 10
shambyross • 10 wrote:

Hello. I am trying to run bowtie2.

This is directly from the Biostarhanbook.

Get reference: ACC-JQ340389 efetch -db=nuccore -format=fasta -id=$ACC >.refs/$ACC.fa $ACC

dwgsim -N 10000 $ACC.fa $ACC

READ1=$ACC.bwa.read1.fastq READ2=$ACC.bwa.read2.fastq

index the reference bowtie2-build $ACC.fa $ACC

Run bowtie2: bowtie2 -x $ACC -1 #READ1 -2 $READ2 | samtools view -h -b | samtools sort > $ACC.bam

THEN I GET THE ERROR: (ERR): Argument expected in next token! Exiting now ...

I do not know what to make of this error and how to fix it.

Can anyone help?

Thanks,

Ross
bowtie line-command • 1.1k views
ADD COMMENT • link •
modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by shambyross • 10
1
gravatar for Devon Ryan
22 months ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

You should post this on the main biostars site.

Anyway, the error is likely that #READ1 should be $READ1.

BTW, you don't need the -h in samtools view -h -b.
ADD COMMENT • link written 22 months ago by Devon Ryan • 1.9k

Sorry I did actually put in $READ1

ADD REPLY • link written 22 months ago by shambyross • 10

IT also give me the following comment about the wrapper:

Command: /Users/rossshamby/src/bowtie2-2.3.0/bowtie2-align-s --wrapper basic-0 -0 (ERR): bowtie2-align exited with value 1

ADD REPLY • link written 22 months ago by shambyross • 10

Devon, the command finally worked. Perhaps it was the -h

ADD REPLY • link written 22 months ago by shambyross • 10
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour