Bowtie2 error with single end mapping
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4.0 years ago
H.Hasani ▴ 980

Dear all,

I'm facing a tedious error and not sure what causing it. I have single-end reads and simply trying to align it using Bowtie2 as follows:

bowtie2 -p 10 --sensitive --no-mixed -t -x my_genome -U my_File.fq.gz -S my_output.sam

When I print this line, everything seems correct, however, Bowtie2 terminates with the following error:

bowtie2-2.2.6/bin/bowtie2-align-s --wrapper basic-0 -p 10 --sensitive --no-mixed -t -x my_genome -S my_output.sam -U /tmp/11841.unp

I forgot to mention the input is completely fine, as I checked it with zcat and it is indeed a correct fastq format.

Can somebody explain this to me and what should I do?

Thanx

ChIP-Seq single-end read mapping • 5.3k views
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2
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I think you forgot to include information about the error (i.e. include more lines around where you are seeing this).

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Not sure why you are using --no-mixed with single end reads though, -U option must take care of single end reads

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  1. What's your actual error? I'm guessing something to do with truncated input.
  2. If you send me the path on slack I can have a look.
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Thank you all. I realized that bowtie2 was not able to access the genome folder.

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2.9 years ago

Hello, You Just try the below command

bowtie2 -x bowtie_index -U read.fastq -S alignment.sam --no-unal

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